Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-10-11 20:38 -0400 (Fri, 11 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | 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: 1.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz |
StartedAt: 2024-10-09 20:57:47 -0400 (Wed, 09 Oct 2024) |
EndedAt: 2024-10-09 20:59:15 -0400 (Wed, 09 Oct 2024) |
EllapsedTime: 88.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BERT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘BERT/DESCRIPTION’ ... OK * this is package ‘BERT’ version ‘1.0.0’ * 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 23.914 1.281 17.456 * 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-3.19-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life" 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") 2024-10-09 20:58:40.075093 INFO::Formatting Data. 2024-10-09 20:58:40.076672 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:40.087548 INFO::Removing potential empty rows and columns 2024-10-09 20:58:40.364369 INFO::Found 0 missing values. 2024-10-09 20:58:40.368062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:40.368718 INFO::Done 2024-10-09 20:58:40.369275 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:40.381707 INFO::Starting hierarchical adjustment 2024-10-09 20:58:40.38259 INFO::Found 3 batches. 2024-10-09 20:58:40.383155 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:40.384299 INFO::Using default BPPARAM 2024-10-09 20:58:40.384856 INFO::Processing subtree level 1 2024-10-09 20:58:40.479252 INFO::Adjusting the last 1 batches sequentially 2024-10-09 20:58:40.481048 INFO::Done 2024-10-09 20:58:40.48173 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:40.484201 INFO::ASW Batch was -0.0355388049664905 prior to batch effect correction and is now -0.0355388049664905 . 2024-10-09 20:58:40.485324 INFO::Total function execution time is 0.411100149154663 s and adjustment time is 0.0986382961273193 s ( 23.99 ) 2024-10-09 20:58:40.499075 INFO::Formatting Data. 2024-10-09 20:58:40.499895 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:40.500804 INFO::Removing potential empty rows and columns 2024-10-09 20:58:40.501887 INFO::Found 0 missing values. 2024-10-09 20:58:40.5028 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. 2024-10-09 20:58:40.513955 INFO::Formatting Data. 2024-10-09 20:58:40.514707 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:40.515605 INFO::Removing potential empty rows and columns 2024-10-09 20:58:40.516628 INFO::Found 0 missing values. 2024-10-09 20:58:40.51754 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. 2024-10-09 20:58:40.533128 INFO::Formatting Data. 2024-10-09 20:58:40.533885 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:40.534761 INFO::Removing potential empty rows and columns 2024-10-09 20:58:40.53579 INFO::Found 0 missing values. 2024-10-09 20:58:40.536697 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. 2024-10-09 20:58:40.541304 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:40.541876 INFO::Done 2024-10-09 20:58:40.542388 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:40.544466 INFO::Starting hierarchical adjustment 2024-10-09 20:58:40.545149 INFO::Found 2 batches. 2024-10-09 20:58:40.545671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:40.546306 INFO::Using default BPPARAM 2024-10-09 20:58:40.546825 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:40.547746 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:40.570236 INFO::Done 2024-10-09 20:58:40.570966 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:40.572963 INFO::ASW Batch was 0.0388820801481758 prior to batch effect correction and is now -0.101518026974583 . 2024-10-09 20:58:40.573752 INFO::Total function execution time is 0.0407042503356934 s and adjustment time is 0.025191068649292 s ( 61.89 ) 2024-10-09 20:58:40.576605 INFO::Formatting Data. 2024-10-09 20:58:40.577226 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:40.585788 INFO::Formatting Data. 2024-10-09 20:58:40.586499 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:40.5874 INFO::Removing potential empty rows and columns 2024-10-09 20:58:40.588434 INFO::Found 0 missing values. 2024-10-09 20:58:40.59126 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:40.591784 INFO::Done 2024-10-09 20:58:40.592302 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:40.594276 INFO::Starting hierarchical adjustment 2024-10-09 20:58:40.594997 INFO::Found 2 batches. 2024-10-09 20:58:40.595515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:40.596111 INFO::Using default BPPARAM 2024-10-09 20:58:40.596627 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:40.597535 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:40.61201 INFO::Done 2024-10-09 20:58:40.61268 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:40.614633 INFO::ASW Batch was 0.0297792576090206 prior to batch effect correction and is now -0.107417718198651 . 2024-10-09 20:58:40.615426 INFO::Total function execution time is 0.0296697616577148 s and adjustment time is 0.0171608924865723 s ( 57.84 ) 2024-10-09 20:58:40.616472 INFO::Formatting Data. 2024-10-09 20:58:40.617085 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:40.617899 INFO::Removing potential empty rows and columns 2024-10-09 20:58:40.618863 INFO::Found 0 missing values. 2024-10-09 20:58:40.621599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:40.622113 INFO::Done 2024-10-09 20:58:40.622602 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:40.624583 INFO::Starting hierarchical adjustment 2024-10-09 20:58:40.625248 INFO::Found 2 batches. 2024-10-09 20:58:40.625738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:40.626315 INFO::Using default BPPARAM 2024-10-09 20:58:40.626809 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:40.627685 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:40.642265 INFO::Done 2024-10-09 20:58:40.642937 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:40.644954 INFO::ASW Batch was 0.0297792576090206 prior to batch effect correction and is now -0.107417718198651 . 2024-10-09 20:58:40.645723 INFO::Total function execution time is 0.0292425155639648 s and adjustment time is 0.017134428024292 s ( 58.59 ) 2024-10-09 20:58:42.853547 INFO::Formatting Data. 2024-10-09 20:58:42.854385 INFO::Recognized SummarizedExperiment 2024-10-09 20:58:42.85494 INFO::Typecasting input to dataframe. 2024-10-09 20:58:42.92819 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:42.929388 INFO::Removing potential empty rows and columns 2024-10-09 20:58:42.932521 INFO::Found 0 missing values. 2024-10-09 20:58:42.938327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:42.938909 INFO::Done 2024-10-09 20:58:42.939373 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:42.9426 INFO::Starting hierarchical adjustment 2024-10-09 20:58:42.943294 INFO::Found 2 batches. 2024-10-09 20:58:42.943773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:42.944916 INFO::Using default BPPARAM 2024-10-09 20:58:42.945399 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:42.946343 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:42.996243 INFO::Done 2024-10-09 20:58:42.996972 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:42.999938 INFO::ASW Batch was 0.00736180877568622 prior to batch effect correction and is now -0.0901355551840951 . 2024-10-09 20:58:43.000676 INFO::Total function execution time is 0.147540330886841 s and adjustment time is 0.0530388355255127 s ( 35.95 ) 2024-10-09 20:58:43.016406 INFO::Formatting Data. 2024-10-09 20:58:43.017128 INFO::Recognized SummarizedExperiment 2024-10-09 20:58:43.017614 INFO::Typecasting input to dataframe. 2024-10-09 20:58:43.025945 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:43.027004 INFO::Removing potential empty rows and columns 2024-10-09 20:58:43.029922 INFO::Found 0 missing values. 2024-10-09 20:58:43.035674 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:43.036203 INFO::Done 2024-10-09 20:58:43.036669 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:43.040011 INFO::Starting hierarchical adjustment 2024-10-09 20:58:43.040682 INFO::Found 2 batches. 2024-10-09 20:58:43.041142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:43.041672 INFO::Using default BPPARAM 2024-10-09 20:58:43.042125 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:43.043049 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:43.070231 INFO::Done 2024-10-09 20:58:43.071111 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:43.074954 INFO::ASW Batch was -0.0160736926781809 prior to batch effect correction and is now -0.0160736926781809 . 2024-10-09 20:58:43.075845 INFO::Total function execution time is 0.0593931674957275 s and adjustment time is 0.0295939445495605 s ( 49.83 ) 2024-10-09 20:58:43.093416 INFO::Formatting Data. 2024-10-09 20:58:43.094182 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:43.095076 INFO::Removing potential empty rows and columns 2024-10-09 20:58:43.096148 INFO::Found 0 missing values. 2024-10-09 20:58:43.098859 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:43.099357 INFO::Done 2024-10-09 20:58:43.099816 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:43.10187 INFO::Starting hierarchical adjustment 2024-10-09 20:58:43.102516 INFO::Found 3 batches. 2024-10-09 20:58:43.103137 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:43.103719 INFO::Using default BPPARAM 2024-10-09 20:58:43.104237 INFO::Processing subtree level 1 2024-10-09 20:58:43.264443 INFO::Adjusting the last 1 batches sequentially 2024-10-09 20:58:43.266731 INFO::Done 2024-10-09 20:58:43.267641 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:43.2708 INFO::ASW Batch was -0.0790112869037823 prior to batch effect correction and is now -0.173114017851459 . 2024-10-09 20:58:43.271899 INFO::Total function execution time is 0.178470611572266 s and adjustment time is 0.164280652999878 s ( 92.05 ) 2024-10-09 20:58:43.289305 INFO::Skipping initial DF formatting 2024-10-09 20:58:43.290072 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:43.294475 INFO::Starting hierarchical adjustment 2024-10-09 20:58:43.295251 INFO::Found 5 batches. 2024-10-09 20:58:43.295801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:43.296483 INFO::Using default BPPARAM 2024-10-09 20:58:43.297035 INFO::Processing subtree level 1 2024-10-09 20:58:43.475941 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:43.478348 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:43.50134 INFO::Done 2024-10-09 20:58:43.502245 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:43.506734 INFO::ASW Batch was 0.520144330127122 prior to batch effect correction and is now 0.520144330127122 . 2024-10-09 20:58:43.507434 INFO::ASW Label was 0.319513002513724 prior to batch effect correction and is now 0.319513002513724 . 2024-10-09 20:58:43.50835 INFO::Total function execution time is 0.219111919403076 s and adjustment time is 0.206197738647461 s ( 94.11 ) 2024-10-09 20:58:43.526942 INFO::Formatting Data. 2024-10-09 20:58:43.527894 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:43.52892 INFO::Removing potential empty rows and columns 2024-10-09 20:58:43.52998 INFO::Found 0 missing values. 2024-10-09 20:58:43.534622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:43.535234 INFO::Done 2024-10-09 20:58:43.535814 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:43.538982 INFO::Starting hierarchical adjustment 2024-10-09 20:58:43.539763 INFO::Found 5 batches. 2024-10-09 20:58:43.540325 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:43.541009 INFO::Using default BPPARAM 2024-10-09 20:58:43.541561 INFO::Processing subtree level 1 2024-10-09 20:58:43.660492 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:43.662709 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:43.680503 INFO::Done 2024-10-09 20:58:43.681288 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:43.684725 INFO::ASW Batch was 0.244225683763656 prior to batch effect correction and is now -0.0647959557257196 . 2024-10-09 20:58:43.685412 INFO::ASW Label was 0.553579384462642 prior to batch effect correction and is now 0.872105566411526 . 2024-10-09 20:58:43.686297 INFO::Total function execution time is 0.159469842910767 s and adjustment time is 0.140879154205322 s ( 88.34 ) 2024-10-09 20:58:43.687204 INFO::Formatting Data. 2024-10-09 20:58:43.687856 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:43.688737 INFO::Removing potential empty rows and columns 2024-10-09 20:58:43.689766 INFO::Found 0 missing values. 2024-10-09 20:58:43.693942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:43.694505 INFO::Done 2024-10-09 20:58:43.695068 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:43.698163 INFO::Starting hierarchical adjustment 2024-10-09 20:58:43.698918 INFO::Found 5 batches. 2024-10-09 20:58:43.699464 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:43.700156 INFO::Using default BPPARAM 2024-10-09 20:58:43.7008 INFO::Processing subtree level 1 2024-10-09 20:58:43.8241 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:43.825886 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:43.843539 INFO::Done 2024-10-09 20:58:43.84434 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:43.847664 INFO::ASW Batch was 0.244225683763656 prior to batch effect correction and is now -0.0647959557257196 . 2024-10-09 20:58:43.848356 INFO::ASW Label was 0.553579384462642 prior to batch effect correction and is now 0.872105566411526 . 2024-10-09 20:58:43.849232 INFO::Total function execution time is 0.162025213241577 s and adjustment time is 0.144745349884033 s ( 89.34 ) 2024-10-09 20:58:43.862679 INFO::Formatting Data. 2024-10-09 20:58:43.863501 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:43.864439 INFO::Removing potential empty rows and columns 2024-10-09 20:58:43.865442 INFO::Found 0 missing values. 2024-10-09 20:58:43.869607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:43.870217 INFO::Done 2024-10-09 20:58:43.870826 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:43.874146 INFO::Starting hierarchical adjustment 2024-10-09 20:58:43.874916 INFO::Found 5 batches. 2024-10-09 20:58:43.875459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:43.876081 INFO::Using default BPPARAM 2024-10-09 20:58:43.876616 INFO::Processing subtree level 1 2024-10-09 20:58:44.007906 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:44.009671 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:44.032963 INFO::Done 2024-10-09 20:58:44.033869 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.037356 INFO::ASW Batch was 0.485327247369713 prior to batch effect correction and is now 0.0575930809215167 . 2024-10-09 20:58:44.03804 INFO::ASW Label was 0.330939379734861 prior to batch effect correction and is now 0.632567752640729 . 2024-10-09 20:58:44.03895 INFO::Total function execution time is 0.176326513290405 s and adjustment time is 0.158129692077637 s ( 89.68 ) 2024-10-09 20:58:44.039902 INFO::Formatting Data. 2024-10-09 20:58:44.040573 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.041507 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.042572 INFO::Found 0 missing values. 2024-10-09 20:58:44.046924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.04752 INFO::Done 2024-10-09 20:58:44.048116 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.051419 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.052196 INFO::Found 5 batches. 2024-10-09 20:58:44.052766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.053418 INFO::Using default BPPARAM 2024-10-09 20:58:44.054033 INFO::Processing subtree level 1 2024-10-09 20:58:44.1864 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:44.188354 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:44.208803 INFO::Done 2024-10-09 20:58:44.209528 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.212756 INFO::ASW Batch was 0.485327247369713 prior to batch effect correction and is now 0.0575930809215167 . 2024-10-09 20:58:44.213401 INFO::ASW Label was 0.330939379734861 prior to batch effect correction and is now 0.632567752640729 . 2024-10-09 20:58:44.214251 INFO::Total function execution time is 0.174327373504639 s and adjustment time is 0.156755924224854 s ( 89.92 ) 2024-10-09 20:58:44.227351 INFO::Formatting Data. 2024-10-09 20:58:44.228169 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.229098 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.230103 INFO::Found 0 missing values. 2024-10-09 20:58:44.232866 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.233401 INFO::Done 2024-10-09 20:58:44.233931 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.236902 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.237628 INFO::Found 2 batches. 2024-10-09 20:58:44.238149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.238771 INFO::Using default BPPARAM 2024-10-09 20:58:44.239329 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:44.240273 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:44.255426 INFO::Done 2024-10-09 20:58:44.256263 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.259311 INFO::ASW Batch was 0.319422776168374 prior to batch effect correction and is now -0.0226462768591626 . 2024-10-09 20:58:44.259907 INFO::ASW Label was 0.690653805778125 prior to batch effect correction and is now 0.919374955061767 . 2024-10-09 20:58:44.260732 INFO::Total function execution time is 0.0334603786468506 s and adjustment time is 0.0178654193878174 s ( 53.39 ) 2024-10-09 20:58:44.26154 INFO::Formatting Data. 2024-10-09 20:58:44.262153 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.263016 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.26397 INFO::Found 0 missing values. 2024-10-09 20:58:44.266631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.267245 INFO::Done 2024-10-09 20:58:44.267757 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.270892 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.271617 INFO::Found 2 batches. 2024-10-09 20:58:44.272138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.272756 INFO::Using default BPPARAM 2024-10-09 20:58:44.273255 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:44.274213 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:44.288873 INFO::Done 2024-10-09 20:58:44.28955 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.313026 INFO::ASW Batch was 0.319422776168374 prior to batch effect correction and is now -0.0226462768591626 . 2024-10-09 20:58:44.313747 INFO::ASW Label was 0.690653805778125 prior to batch effect correction and is now 0.919374955061767 . 2024-10-09 20:58:44.314592 INFO::Total function execution time is 0.0530471801757812 s and adjustment time is 0.0173704624176025 s ( 32.75 ) 2024-10-09 20:58:44.326086 INFO::Formatting Data. 2024-10-09 20:58:44.326884 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.327854 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.328863 INFO::Found 0 missing values. 2024-10-09 20:58:44.331215 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.331784 INFO::Done 2024-10-09 20:58:44.332315 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.33442 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.335195 INFO::Found 2 batches. 2024-10-09 20:58:44.335765 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.33637 INFO::Using default BPPARAM 2024-10-09 20:58:44.336951 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:44.337878 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:44.372133 INFO::Done 2024-10-09 20:58:44.372907 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.375297 INFO::ASW Batch was -0.0927910193450122 prior to batch effect correction and is now -0.190117658083908 . 2024-10-09 20:58:44.376247 INFO::Total function execution time is 0.0502181053161621 s and adjustment time is 0.0370678901672363 s ( 73.81 ) 2024-10-09 20:58:44.388856 INFO::Formatting Data. 2024-10-09 20:58:44.389739 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.390674 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.391798 INFO::Found 0 missing values. 2024-10-09 20:58:44.393107 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. 2024-10-09 20:58:44.398247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.398888 INFO::Done 2024-10-09 20:58:44.399462 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.402761 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.403538 INFO::Found 2 batches. 2024-10-09 20:58:44.404068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.404673 INFO::Using default BPPARAM 2024-10-09 20:58:44.405206 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:44.40625 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:44.424474 INFO::Done 2024-10-09 20:58:44.425185 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.428326 INFO::ASW Batch was 0.434200249352059 prior to batch effect correction and is now 0.0249764624674079 . 2024-10-09 20:58:44.429023 INFO::ASW Label was 0.602521079451412 prior to batch effect correction and is now 0.928409379166451 . 2024-10-09 20:58:44.429831 INFO::Total function execution time is 0.0410816669464111 s and adjustment time is 0.0210745334625244 s ( 51.3 ) 2024-10-09 20:58:44.430651 INFO::Formatting Data. 2024-10-09 20:58:44.431271 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.43217 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.433205 INFO::Found 0 missing values. 2024-10-09 20:58:44.434067 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. 2024-10-09 20:58:44.438593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.441842 INFO::Done 2024-10-09 20:58:44.442521 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.446249 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.447004 INFO::Found 2 batches. 2024-10-09 20:58:44.447553 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.448227 INFO::Using default BPPARAM 2024-10-09 20:58:44.448811 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:44.449829 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:44.469683 INFO::Done 2024-10-09 20:58:44.470417 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.473556 INFO::ASW Batch was 0.434200249352059 prior to batch effect correction and is now 0.0249764624674079 . 2024-10-09 20:58:44.47422 INFO::ASW Label was 0.602521079451412 prior to batch effect correction and is now 0.928409379166451 . 2024-10-09 20:58:44.475137 INFO::Total function execution time is 0.0444653034210205 s and adjustment time is 0.0228440761566162 s ( 51.38 ) 2024-10-09 20:58:44.682024 INFO::Formatting Data. 2024-10-09 20:58:44.682883 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.683892 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.684993 INFO::Found 0 missing values. 2024-10-09 20:58:44.688052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.688598 INFO::Done 2024-10-09 20:58:44.689116 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.691157 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.691867 INFO::Found 3 batches. 2024-10-09 20:58:44.692387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.69298 INFO::Using default BPPARAM 2024-10-09 20:58:44.693521 INFO::Processing subtree level 1 2024-10-09 20:58:44.787045 INFO::Adjusting the last 1 batches sequentially 2024-10-09 20:58:44.788967 INFO::Done 2024-10-09 20:58:44.789801 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.792715 INFO::ASW Batch was 0.0529422755082853 prior to batch effect correction and is now 0.0529422755082853 . 2024-10-09 20:58:44.793791 INFO::Total function execution time is 0.111780881881714 s and adjustment time is 0.0972006320953369 s ( 86.96 ) 2024-10-09 20:58:44.795067 INFO::Formatting Data. 2024-10-09 20:58:44.795772 INFO::Typecasting input to dataframe. 2024-10-09 20:58:44.796589 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.797607 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.798766 INFO::Found 0 missing values. 2024-10-09 20:58:44.802041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.802696 INFO::Done 2024-10-09 20:58:44.803337 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.805572 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.806345 INFO::Found 3 batches. 2024-10-09 20:58:44.806858 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.807463 INFO::Using default BPPARAM 2024-10-09 20:58:44.808015 INFO::Processing subtree level 1 2024-10-09 20:58:44.898556 INFO::Adjusting the last 1 batches sequentially 2024-10-09 20:58:44.90051 INFO::Done 2024-10-09 20:58:44.901206 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:44.903894 INFO::ASW Batch was 0.0529422755082853 prior to batch effect correction and is now 0.0529422755082853 . 2024-10-09 20:58:44.9049 INFO::Total function execution time is 0.109848022460938 s and adjustment time is 0.094294548034668 s ( 85.84 ) 2024-10-09 20:58:44.920945 INFO::Formatting Data. 2024-10-09 20:58:44.921896 INFO::Typecasting input to dataframe. 2024-10-09 20:58:44.922839 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:44.923868 INFO::Removing potential empty rows and columns 2024-10-09 20:58:44.925028 INFO::Found 0 missing values. 2024-10-09 20:58:44.928131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:44.928686 INFO::Done 2024-10-09 20:58:44.929233 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:44.931615 INFO::Starting hierarchical adjustment 2024-10-09 20:58:44.932403 INFO::Found 3 batches. 2024-10-09 20:58:44.932938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:44.93357 INFO::Using default BPPARAM 2024-10-09 20:58:44.934096 INFO::Processing subtree level 1 2024-10-09 20:58:45.027212 INFO::Adjusting the last 1 batches sequentially 2024-10-09 20:58:45.029061 INFO::Done 2024-10-09 20:58:45.029775 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:45.032341 INFO::ASW Batch was -0.165746552941127 prior to batch effect correction and is now -0.165746552941127 . 2024-10-09 20:58:45.033293 INFO::Total function execution time is 0.112435340881348 s and adjustment time is 0.0967984199523926 s ( 86.09 ) 2024-10-09 20:58:45.185338 INFO::Formatting Data. 2024-10-09 20:58:45.186234 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:45.187382 INFO::Removing potential empty rows and columns 2024-10-09 20:58:45.190126 INFO::Found 1000 missing values. 2024-10-09 20:58:45.207632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:45.208368 INFO::Done 2024-10-09 20:58:45.208912 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:45.214369 INFO::Starting hierarchical adjustment 2024-10-09 20:58:45.215147 INFO::Found 10 batches. 2024-10-09 20:58:45.215664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:45.216319 INFO::Using default BPPARAM 2024-10-09 20:58:45.216834 INFO::Processing subtree level 1 2024-10-09 20:58:45.447208 INFO::Processing subtree level 2 2024-10-09 20:58:45.686175 INFO::Adjusting the last 1 batches sequentially 2024-10-09 20:58:45.688738 INFO::Done 2024-10-09 20:58:45.689688 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:45.696013 INFO::ASW Batch was 0.466137575136675 prior to batch effect correction and is now 0.466137575136675 . 2024-10-09 20:58:45.696801 INFO::ASW Label was 0.330054633364995 prior to batch effect correction and is now 0.330054633364995 . 2024-10-09 20:58:45.697788 INFO::Total function execution time is 0.512544870376587 s and adjustment time is 0.473661184310913 s ( 92.41 ) 2024-10-09 20:58:45.69873 INFO::Formatting Data. 2024-10-09 20:58:45.699435 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:45.700929 INFO::Removing potential empty rows and columns 2024-10-09 20:58:45.704325 INFO::Found 1000 missing values. 2024-10-09 20:58:45.731821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:45.732897 INFO::Done 2024-10-09 20:58:45.73357 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:45.739698 INFO::Starting hierarchical adjustment 2024-10-09 20:58:45.740545 INFO::Found 10 batches. 2024-10-09 20:58:47.025992 INFO::Set up parallel execution backend with 2 workers 2024-10-09 20:58:47.027794 INFO::Processing subtree level 1 with 10 batches using 2 cores. 2024-10-09 20:58:48.145456 INFO::Adjusting the last 2 batches sequentially 2024-10-09 20:58:48.146977 INFO::Adjusting sequential tree level 1 with 2 batches 2024-10-09 20:58:48.162555 INFO::Done 2024-10-09 20:58:48.16322 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:48.167826 INFO::ASW Batch was 0.466137575136675 prior to batch effect correction and is now 0.466137575136675 . 2024-10-09 20:58:48.168372 INFO::ASW Label was 0.330054633364995 prior to batch effect correction and is now 0.330054633364995 . 2024-10-09 20:58:48.16912 INFO::Total function execution time is 2.4704487323761 s and adjustment time is 2.42218589782715 s ( 98.05 ) 2024-10-09 20:58:48.303573 INFO::Formatting Data. 2024-10-09 20:58:48.304347 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.305198 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.30622 INFO::Found 0 missing values. 2024-10-09 20:58:48.309596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.310114 INFO::Done 2024-10-09 20:58:48.310589 INFO::Acquiring quality metrics before batch effect correction. 2024-10-09 20:58:48.313229 INFO::Starting hierarchical adjustment 2024-10-09 20:58:48.313889 INFO::Found 3 batches. 2024-10-09 20:58:48.314392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-10-09 20:58:48.315016 INFO::Using default BPPARAM 2024-10-09 20:58:48.315524 INFO::Processing subtree level 1 2024-10-09 20:58:48.414068 INFO::Adjusting the last 1 batches sequentially 2024-10-09 20:58:48.415959 INFO::Done 2024-10-09 20:58:48.416659 INFO::Acquiring quality metrics after batch effect correction. 2024-10-09 20:58:48.419919 INFO::ASW Batch was 0.158986665642041 prior to batch effect correction and is now -0.140103056222758 . 2024-10-09 20:58:48.420534 INFO::ASW Label was -0.168222176476914 prior to batch effect correction and is now 0.0337501789875301 . 2024-10-09 20:58:48.421418 INFO::Total function execution time is 0.117899656295776 s and adjustment time is 0.102169036865234 s ( 86.66 ) 2024-10-09 20:58:48.530043 INFO::Formatting Data. 2024-10-09 20:58:48.530872 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.53179 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.532794 INFO::Found 2 missing values. 2024-10-09 20:58:48.535458 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.535973 INFO::Done 2024-10-09 20:58:48.560509 INFO::Found NA in Reference column 2024-10-09 20:58:48.56884 INFO::Require at least two references per batch. 2024-10-09 20:58:48.587102 INFO::Formatting Data. 2024-10-09 20:58:48.58781 INFO::Recognized SummarizedExperiment 2024-10-09 20:58:48.588313 INFO::Typecasting input to dataframe. 2024-10-09 20:58:48.597209 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.598295 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.601485 INFO::Found 0 missing values. 2024-10-09 20:58:48.61238 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.61311 INFO::Done 2024-10-09 20:58:48.6282 INFO::Formatting Data. 2024-10-09 20:58:48.628914 INFO::Recognized SummarizedExperiment 2024-10-09 20:58:48.629459 INFO::Typecasting input to dataframe. 2024-10-09 20:58:48.646605 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.647892 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.651446 INFO::Found 0 missing values. 2024-10-09 20:58:48.662386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.663113 INFO::Done 2024-10-09 20:58:48.678121 INFO::Formatting Data. 2024-10-09 20:58:48.678861 INFO::Recognized SummarizedExperiment 2024-10-09 20:58:48.679413 INFO::Typecasting input to dataframe. 2024-10-09 20:58:48.696693 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.697801 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.698973 INFO::Found 0 missing values. 2024-10-09 20:58:48.699911 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. 2024-10-09 20:58:48.704737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.705274 INFO::Done 2024-10-09 20:58:48.715935 INFO::Formatting Data. 2024-10-09 20:58:48.716747 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.717663 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.718719 INFO::Found 0 missing values. 2024-10-09 20:58:48.721928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.722541 INFO::Done 2024-10-09 20:58:48.733837 INFO::Formatting Data. 2024-10-09 20:58:48.734632 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.735619 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.736643 INFO::Found 0 missing values. 2024-10-09 20:58:48.739727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.740275 INFO::Done 2024-10-09 20:58:48.76872 INFO::Formatting Data. 2024-10-09 20:58:48.769558 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.770597 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.771745 INFO::Found 1 missing values. 2024-10-09 20:58:48.774236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.774747 INFO::Done 2024-10-09 20:58:48.794369 INFO::Formatting Data. 2024-10-09 20:58:48.795319 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.796336 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.797602 INFO::Found 2 missing values. 2024-10-09 20:58:48.798665 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. 2024-10-09 20:58:48.801357 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.801986 INFO::Done 2024-10-09 20:58:48.813714 INFO::Formatting Data. 2024-10-09 20:58:48.814521 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.815553 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.816659 INFO::Found 2 missing values. 2024-10-09 20:58:48.818567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.819178 INFO::Done 2024-10-09 20:58:48.831767 INFO::Formatting Data. 2024-10-09 20:58:48.832719 INFO::Typecasting input to dataframe. 2024-10-09 20:58:48.833754 INFO::Replacing NaNs with NAs. 2024-10-09 20:58:48.834835 INFO::Removing potential empty rows and columns 2024-10-09 20:58:48.836123 INFO::Found 0 missing values. 2024-10-09 20:58:48.839716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-10-09 20:58:48.840327 INFO::Done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ] > > proc.time() user system elapsed 17.065 4.173 20.810
BERT.Rcheck/BERT-Ex.timings
name | user | system | elapsed | |
BERT | 23.914 | 1.281 | 17.456 | |
compute_asw | 0.021 | 0.004 | 0.025 | |
count_existing | 0.015 | 0.000 | 0.014 | |
generate_data_covariables | 0.012 | 0.000 | 0.013 | |
generate_dataset | 0.008 | 0.004 | 0.012 | |