Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:38:53 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 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 | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz |
StartedAt: 2024-05-03 20:19:00 -0400 (Fri, 03 May 2024) |
EndedAt: 2024-05-03 20:20:24 -0400 (Fri, 03 May 2024) |
EllapsedTime: 83.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BERT.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BERT 27.551 1.633 19.82 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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") 2024-05-03 20:20:03.100859 INFO::Formatting Data. 2024-05-03 20:20:03.10471 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:03.116437 INFO::Removing potential empty rows and columns 2024-05-03 20:20:03.402852 INFO::Found 0 missing values. 2024-05-03 20:20:03.406263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:03.40688 INFO::Done 2024-05-03 20:20:03.407399 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:03.421779 INFO::Starting hierarchical adjustment 2024-05-03 20:20:03.422903 INFO::Found 3 batches. 2024-05-03 20:20:03.423598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:03.425132 INFO::Using default BPPARAM 2024-05-03 20:20:03.425967 INFO::Processing subtree level 1 2024-05-03 20:20:03.583302 INFO::Adjusting the last 1 batches sequentially 2024-05-03 20:20:03.587814 INFO::Done 2024-05-03 20:20:03.588811 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:03.595477 INFO::ASW Batch was -0.120286556723252 prior to batch effect correction and is now -0.120286556723252 . 2024-05-03 20:20:03.597599 INFO::Total function execution time is 0.497148036956787 s and adjustment time is 0.165104866027832 s ( 33.21 ) 2024-05-03 20:20:03.620309 INFO::Formatting Data. 2024-05-03 20:20:03.621653 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:03.623209 INFO::Removing potential empty rows and columns 2024-05-03 20:20:03.62475 INFO::Found 0 missing values. 2024-05-03 20:20:03.626199 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. 2024-05-03 20:20:03.643036 INFO::Formatting Data. 2024-05-03 20:20:03.644105 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:03.645385 INFO::Removing potential empty rows and columns 2024-05-03 20:20:03.646872 INFO::Found 0 missing values. 2024-05-03 20:20:03.648474 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. 2024-05-03 20:20:03.671719 INFO::Formatting Data. 2024-05-03 20:20:03.672531 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:03.673394 INFO::Removing potential empty rows and columns 2024-05-03 20:20:03.674328 INFO::Found 0 missing values. 2024-05-03 20:20:03.67519 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. 2024-05-03 20:20:03.679072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:03.679589 INFO::Done 2024-05-03 20:20:03.680052 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:03.681907 INFO::Starting hierarchical adjustment 2024-05-03 20:20:03.682541 INFO::Found 2 batches. 2024-05-03 20:20:03.683009 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:03.683578 INFO::Using default BPPARAM 2024-05-03 20:20:03.684035 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:03.68485 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:03.708432 INFO::Done 2024-05-03 20:20:03.709081 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:03.710927 INFO::ASW Batch was -0.057844070779596 prior to batch effect correction and is now -0.103721863768822 . 2024-05-03 20:20:03.711655 INFO::Total function execution time is 0.0400331020355225 s and adjustment time is 0.0259909629821777 s ( 64.92 ) 2024-05-03 20:20:03.714223 INFO::Formatting Data. 2024-05-03 20:20:03.714819 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:03.724083 INFO::Formatting Data. 2024-05-03 20:20:03.725125 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:03.726371 INFO::Removing potential empty rows and columns 2024-05-03 20:20:03.727807 INFO::Found 0 missing values. 2024-05-03 20:20:03.732075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:03.73286 INFO::Done 2024-05-03 20:20:03.733578 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:03.736239 INFO::Starting hierarchical adjustment 2024-05-03 20:20:03.737173 INFO::Found 2 batches. 2024-05-03 20:20:03.737876 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:03.738663 INFO::Using default BPPARAM 2024-05-03 20:20:03.73936 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:03.740803 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:03.764995 INFO::Done 2024-05-03 20:20:03.765978 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:03.768843 INFO::ASW Batch was 0.0724735123027953 prior to batch effect correction and is now -0.0998347410357455 . 2024-05-03 20:20:03.769976 INFO::Total function execution time is 0.0459609031677246 s and adjustment time is 0.0279688835144043 s ( 60.85 ) 2024-05-03 20:20:03.771037 INFO::Formatting Data. 2024-05-03 20:20:03.771629 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:03.773103 INFO::Removing potential empty rows and columns 2024-05-03 20:20:03.774365 INFO::Found 0 missing values. 2024-05-03 20:20:03.778365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:03.779264 INFO::Done 2024-05-03 20:20:03.780231 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:03.782194 INFO::Starting hierarchical adjustment 2024-05-03 20:20:03.782821 INFO::Found 2 batches. 2024-05-03 20:20:03.783294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:03.78382 INFO::Using default BPPARAM 2024-05-03 20:20:03.784276 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:03.7851 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:03.80535 INFO::Done 2024-05-03 20:20:03.806259 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:03.808224 INFO::ASW Batch was 0.0724735123027953 prior to batch effect correction and is now -0.0998347410357455 . 2024-05-03 20:20:03.809002 INFO::Total function execution time is 0.0379848480224609 s and adjustment time is 0.0225839614868164 s ( 59.46 ) 2024-05-03 20:20:06.396464 INFO::Formatting Data. 2024-05-03 20:20:06.397465 INFO::Recognized SummarizedExperiment 2024-05-03 20:20:06.398229 INFO::Typecasting input to dataframe. 2024-05-03 20:20:07.255469 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:07.256739 INFO::Removing potential empty rows and columns 2024-05-03 20:20:07.259488 INFO::Found 0 missing values. 2024-05-03 20:20:07.266406 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:07.267041 INFO::Done 2024-05-03 20:20:07.2677 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:07.270949 INFO::Starting hierarchical adjustment 2024-05-03 20:20:07.271535 INFO::Found 2 batches. 2024-05-03 20:20:07.271994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:07.273024 INFO::Using default BPPARAM 2024-05-03 20:20:07.273504 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:07.274431 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:07.32178 INFO::Done 2024-05-03 20:20:07.322666 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:07.327261 INFO::ASW Batch was -0.00653190866031194 prior to batch effect correction and is now -0.0886143803572082 . 2024-05-03 20:20:07.328353 INFO::Total function execution time is 0.932377815246582 s and adjustment time is 0.0502808094024658 s ( 5.39 ) 2024-05-03 20:20:07.352122 INFO::Formatting Data. 2024-05-03 20:20:07.352869 INFO::Recognized SummarizedExperiment 2024-05-03 20:20:07.353455 INFO::Typecasting input to dataframe. 2024-05-03 20:20:07.360977 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:07.361977 INFO::Removing potential empty rows and columns 2024-05-03 20:20:07.364573 INFO::Found 0 missing values. 2024-05-03 20:20:07.370973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:07.371539 INFO::Done 2024-05-03 20:20:07.3725 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:07.376362 INFO::Starting hierarchical adjustment 2024-05-03 20:20:07.377382 INFO::Found 2 batches. 2024-05-03 20:20:07.378109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:07.378898 INFO::Using default BPPARAM 2024-05-03 20:20:07.379557 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:07.380906 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:07.411179 INFO::Done 2024-05-03 20:20:07.412059 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:07.41679 INFO::ASW Batch was 0.00772545005685677 prior to batch effect correction and is now 0.00772545005685677 . 2024-05-03 20:20:07.417657 INFO::Total function execution time is 0.0654420852661133 s and adjustment time is 0.0339550971984863 s ( 51.89 ) 2024-05-03 20:20:07.43997 INFO::Formatting Data. 2024-05-03 20:20:07.440865 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:07.441968 INFO::Removing potential empty rows and columns 2024-05-03 20:20:07.44283 INFO::Found 0 missing values. 2024-05-03 20:20:07.446827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:07.447628 INFO::Done 2024-05-03 20:20:07.44831 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:07.450667 INFO::Starting hierarchical adjustment 2024-05-03 20:20:07.451264 INFO::Found 3 batches. 2024-05-03 20:20:07.451686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:07.452303 INFO::Using default BPPARAM 2024-05-03 20:20:07.453254 INFO::Processing subtree level 1 2024-05-03 20:20:07.760561 INFO::Adjusting the last 1 batches sequentially 2024-05-03 20:20:07.768699 INFO::Done 2024-05-03 20:20:07.769808 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:07.776102 INFO::ASW Batch was -0.0166363160470837 prior to batch effect correction and is now -0.181465454160527 . 2024-05-03 20:20:07.779968 INFO::Total function execution time is 0.339025974273682 s and adjustment time is 0.31746506690979 s ( 93.64 ) 2024-05-03 20:20:07.805826 INFO::Skipping initial DF formatting 2024-05-03 20:20:07.806565 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:07.811098 INFO::Starting hierarchical adjustment 2024-05-03 20:20:07.812298 INFO::Found 5 batches. 2024-05-03 20:20:07.812861 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:07.81345 INFO::Using default BPPARAM 2024-05-03 20:20:07.813938 INFO::Processing subtree level 1 2024-05-03 20:20:08.046999 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:08.05923 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:08.10123 INFO::Done 2024-05-03 20:20:08.101942 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:08.107558 INFO::ASW Batch was 0.483339960802334 prior to batch effect correction and is now 0.483339960802334 . 2024-05-03 20:20:08.108376 INFO::ASW Label was 0.400253892629455 prior to batch effect correction and is now 0.400253892629455 . 2024-05-03 20:20:08.109426 INFO::Total function execution time is 0.303670883178711 s and adjustment time is 0.289189100265503 s ( 95.23 ) 2024-05-03 20:20:08.137345 INFO::Formatting Data. 2024-05-03 20:20:08.138533 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:08.139793 INFO::Removing potential empty rows and columns 2024-05-03 20:20:08.140977 INFO::Found 0 missing values. 2024-05-03 20:20:08.145426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:08.146034 INFO::Done 2024-05-03 20:20:08.146532 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:08.150126 INFO::Starting hierarchical adjustment 2024-05-03 20:20:08.150942 INFO::Found 5 batches. 2024-05-03 20:20:08.151554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:08.152575 INFO::Using default BPPARAM 2024-05-03 20:20:08.153278 INFO::Processing subtree level 1 2024-05-03 20:20:08.297752 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:08.326493 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:08.360402 INFO::Done 2024-05-03 20:20:08.361208 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:08.365572 INFO::ASW Batch was 0.388321850507152 prior to batch effect correction and is now 0.0217418629085879 . 2024-05-03 20:20:08.366831 INFO::ASW Label was 0.402434912199033 prior to batch effect correction and is now 0.713127102926085 . 2024-05-03 20:20:08.368518 INFO::Total function execution time is 0.231243133544922 s and adjustment time is 0.209626913070679 s ( 90.65 ) 2024-05-03 20:20:08.369838 INFO::Formatting Data. 2024-05-03 20:20:08.370696 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:08.371652 INFO::Removing potential empty rows and columns 2024-05-03 20:20:08.37265 INFO::Found 0 missing values. 2024-05-03 20:20:08.376615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:08.377118 INFO::Done 2024-05-03 20:20:08.377609 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:08.38117 INFO::Starting hierarchical adjustment 2024-05-03 20:20:08.382015 INFO::Found 5 batches. 2024-05-03 20:20:08.382501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:08.383735 INFO::Using default BPPARAM 2024-05-03 20:20:08.384365 INFO::Processing subtree level 1 2024-05-03 20:20:08.535353 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:08.552826 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:08.589299 INFO::Done 2024-05-03 20:20:08.590251 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:08.594211 INFO::ASW Batch was 0.388321850507152 prior to batch effect correction and is now 0.0217418629085879 . 2024-05-03 20:20:08.595938 INFO::ASW Label was 0.402434912199033 prior to batch effect correction and is now 0.713127102926085 . 2024-05-03 20:20:08.597285 INFO::Total function execution time is 0.227377891540527 s and adjustment time is 0.207360029220581 s ( 91.2 ) 2024-05-03 20:20:08.61749 INFO::Formatting Data. 2024-05-03 20:20:08.618226 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:08.620313 INFO::Removing potential empty rows and columns 2024-05-03 20:20:08.621769 INFO::Found 0 missing values. 2024-05-03 20:20:08.628447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:08.629442 INFO::Done 2024-05-03 20:20:08.630427 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:08.635304 INFO::Starting hierarchical adjustment 2024-05-03 20:20:08.63607 INFO::Found 5 batches. 2024-05-03 20:20:08.636574 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:08.63713 INFO::Using default BPPARAM 2024-05-03 20:20:08.637621 INFO::Processing subtree level 1 2024-05-03 20:20:08.764074 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:08.785646 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:08.820887 INFO::Done 2024-05-03 20:20:08.82175 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:08.828126 INFO::ASW Batch was 0.321707222704228 prior to batch effect correction and is now -0.0975173017115611 . 2024-05-03 20:20:08.829381 INFO::ASW Label was 0.24791787527603 prior to batch effect correction and is now 0.826398321893765 . 2024-05-03 20:20:08.831802 INFO::Total function execution time is 0.214236974716187 s and adjustment time is 0.184905052185059 s ( 86.31 ) 2024-05-03 20:20:08.832743 INFO::Formatting Data. 2024-05-03 20:20:08.833714 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:08.834923 INFO::Removing potential empty rows and columns 2024-05-03 20:20:08.835845 INFO::Found 0 missing values. 2024-05-03 20:20:08.84072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:08.841632 INFO::Done 2024-05-03 20:20:08.842388 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:08.846843 INFO::Starting hierarchical adjustment 2024-05-03 20:20:08.847778 INFO::Found 5 batches. 2024-05-03 20:20:08.848513 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:08.849491 INFO::Using default BPPARAM 2024-05-03 20:20:08.85026 INFO::Processing subtree level 1 2024-05-03 20:20:09.011677 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:09.021995 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:09.049463 INFO::Done 2024-05-03 20:20:09.050471 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.054854 INFO::ASW Batch was 0.321707222704228 prior to batch effect correction and is now -0.0975173017115611 . 2024-05-03 20:20:09.055509 INFO::ASW Label was 0.24791787527603 prior to batch effect correction and is now 0.826398321893765 . 2024-05-03 20:20:09.056443 INFO::Total function execution time is 0.223758935928345 s and adjustment time is 0.201925992965698 s ( 90.24 ) 2024-05-03 20:20:09.080465 INFO::Formatting Data. 2024-05-03 20:20:09.081219 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.082964 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.08394 INFO::Found 0 missing values. 2024-05-03 20:20:09.086622 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.087969 INFO::Done 2024-05-03 20:20:09.088722 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.091661 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.092306 INFO::Found 2 batches. 2024-05-03 20:20:09.092756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.09332 INFO::Using default BPPARAM 2024-05-03 20:20:09.094635 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:09.09548 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:09.112942 INFO::Done 2024-05-03 20:20:09.113768 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.116512 INFO::ASW Batch was 0.172295345794398 prior to batch effect correction and is now 0.00770917301012675 . 2024-05-03 20:20:09.117423 INFO::ASW Label was 0.817258247890259 prior to batch effect correction and is now 0.932371105680503 . 2024-05-03 20:20:09.118679 INFO::Total function execution time is 0.0382671356201172 s and adjustment time is 0.0206770896911621 s ( 54.03 ) 2024-05-03 20:20:09.119424 INFO::Formatting Data. 2024-05-03 20:20:09.119964 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.120776 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.121904 INFO::Found 0 missing values. 2024-05-03 20:20:09.125887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.126397 INFO::Done 2024-05-03 20:20:09.12686 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.129357 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.1303 INFO::Found 2 batches. 2024-05-03 20:20:09.131211 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.131878 INFO::Using default BPPARAM 2024-05-03 20:20:09.1326 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:09.133993 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:09.147594 INFO::Done 2024-05-03 20:20:09.148203 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.150675 INFO::ASW Batch was 0.172295345794398 prior to batch effect correction and is now 0.00770917301012675 . 2024-05-03 20:20:09.151204 INFO::ASW Label was 0.817258247890259 prior to batch effect correction and is now 0.932371105680503 . 2024-05-03 20:20:09.151884 INFO::Total function execution time is 0.0324921607971191 s and adjustment time is 0.017719030380249 s ( 54.53 ) 2024-05-03 20:20:09.168789 INFO::Formatting Data. 2024-05-03 20:20:09.169835 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.1711 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.172336 INFO::Found 0 missing values. 2024-05-03 20:20:09.175968 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.176707 INFO::Done 2024-05-03 20:20:09.177377 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.179848 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.18079 INFO::Found 2 batches. 2024-05-03 20:20:09.181471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.182263 INFO::Using default BPPARAM 2024-05-03 20:20:09.182941 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:09.184122 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:09.216079 INFO::Done 2024-05-03 20:20:09.21671 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.218714 INFO::ASW Batch was -0.0766885069280361 prior to batch effect correction and is now -0.147876115971728 . 2024-05-03 20:20:09.219857 INFO::Total function execution time is 0.0511898994445801 s and adjustment time is 0.0355069637298584 s ( 69.36 ) 2024-05-03 20:20:09.237486 INFO::Formatting Data. 2024-05-03 20:20:09.238171 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.238948 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.239999 INFO::Found 0 missing values. 2024-05-03 20:20:09.241295 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. 2024-05-03 20:20:09.246329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.246859 INFO::Done 2024-05-03 20:20:09.247351 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.250169 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.250792 INFO::Found 2 batches. 2024-05-03 20:20:09.251277 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.251798 INFO::Using default BPPARAM 2024-05-03 20:20:09.252237 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:09.253071 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:09.27287 INFO::Done 2024-05-03 20:20:09.273814 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.277847 INFO::ASW Batch was 0.636988876765494 prior to batch effect correction and is now 0.00533337824906933 . 2024-05-03 20:20:09.278452 INFO::ASW Label was 0.342694149461207 prior to batch effect correction and is now 0.896514689612021 . 2024-05-03 20:20:09.279311 INFO::Total function execution time is 0.0418450832366943 s and adjustment time is 0.0221209526062012 s ( 52.86 ) 2024-05-03 20:20:09.280489 INFO::Formatting Data. 2024-05-03 20:20:09.281179 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.282185 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.283659 INFO::Found 0 missing values. 2024-05-03 20:20:09.284511 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. 2024-05-03 20:20:09.289993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.290736 INFO::Done 2024-05-03 20:20:09.291513 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.295005 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.296027 INFO::Found 2 batches. 2024-05-03 20:20:09.296813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.297741 INFO::Using default BPPARAM 2024-05-03 20:20:09.298505 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:09.300014 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:09.321904 INFO::Done 2024-05-03 20:20:09.322555 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.326849 INFO::ASW Batch was 0.636988876765494 prior to batch effect correction and is now 0.00533337824906933 . 2024-05-03 20:20:09.327607 INFO::ASW Label was 0.342694149461207 prior to batch effect correction and is now 0.896514689612021 . 2024-05-03 20:20:09.328877 INFO::Total function execution time is 0.0483479499816895 s and adjustment time is 0.0261011123657227 s ( 53.99 ) 2024-05-03 20:20:09.590686 INFO::Formatting Data. 2024-05-03 20:20:09.59139 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.592178 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.593041 INFO::Found 0 missing values. 2024-05-03 20:20:09.596042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.596569 INFO::Done 2024-05-03 20:20:09.597016 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.599253 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.600343 INFO::Found 3 batches. 2024-05-03 20:20:09.601046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.601844 INFO::Using default BPPARAM 2024-05-03 20:20:09.60254 INFO::Processing subtree level 1 2024-05-03 20:20:09.745496 INFO::Adjusting the last 1 batches sequentially 2024-05-03 20:20:09.754013 INFO::Done 2024-05-03 20:20:09.75672 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.765346 INFO::ASW Batch was -0.0138208720575524 prior to batch effect correction and is now -0.0138208720575524 . 2024-05-03 20:20:09.767499 INFO::Total function execution time is 0.176122903823853 s and adjustment time is 0.153844118118286 s ( 87.35 ) 2024-05-03 20:20:09.770051 INFO::Formatting Data. 2024-05-03 20:20:09.771106 INFO::Typecasting input to dataframe. 2024-05-03 20:20:09.772355 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.774284 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.775667 INFO::Found 0 missing values. 2024-05-03 20:20:09.78018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.78086 INFO::Done 2024-05-03 20:20:09.781772 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.784714 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.786076 INFO::Found 3 batches. 2024-05-03 20:20:09.786728 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.787846 INFO::Using default BPPARAM 2024-05-03 20:20:09.788356 INFO::Processing subtree level 1 2024-05-03 20:20:09.916398 INFO::Adjusting the last 1 batches sequentially 2024-05-03 20:20:09.927813 INFO::Done 2024-05-03 20:20:09.930183 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:09.938864 INFO::ASW Batch was -0.0138208720575524 prior to batch effect correction and is now -0.0138208720575524 . 2024-05-03 20:20:09.940967 INFO::Total function execution time is 0.17094087600708 s and adjustment time is 0.141853094100952 s ( 82.98 ) 2024-05-03 20:20:09.969501 INFO::Formatting Data. 2024-05-03 20:20:09.97106 INFO::Typecasting input to dataframe. 2024-05-03 20:20:09.971993 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:09.972916 INFO::Removing potential empty rows and columns 2024-05-03 20:20:09.975561 INFO::Found 0 missing values. 2024-05-03 20:20:09.978628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:09.979182 INFO::Done 2024-05-03 20:20:09.979653 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:09.981457 INFO::Starting hierarchical adjustment 2024-05-03 20:20:09.982067 INFO::Found 3 batches. 2024-05-03 20:20:09.982545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:09.983388 INFO::Using default BPPARAM 2024-05-03 20:20:09.983858 INFO::Processing subtree level 1 2024-05-03 20:20:10.105517 INFO::Adjusting the last 1 batches sequentially 2024-05-03 20:20:10.116881 INFO::Done 2024-05-03 20:20:10.119403 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:10.129952 INFO::ASW Batch was -0.10010154303703 prior to batch effect correction and is now -0.10010154303703 . 2024-05-03 20:20:10.134045 INFO::Total function execution time is 0.164990901947021 s and adjustment time is 0.134835004806519 s ( 81.72 ) 2024-05-03 20:20:10.374772 INFO::Formatting Data. 2024-05-03 20:20:10.376157 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:10.378509 INFO::Removing potential empty rows and columns 2024-05-03 20:20:10.382711 INFO::Found 1000 missing values. 2024-05-03 20:20:10.406926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:10.407805 INFO::Done 2024-05-03 20:20:10.409119 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:10.417047 INFO::Starting hierarchical adjustment 2024-05-03 20:20:10.418004 INFO::Found 10 batches. 2024-05-03 20:20:10.418788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:10.419475 INFO::Using default BPPARAM 2024-05-03 20:20:10.420326 INFO::Processing subtree level 1 2024-05-03 20:20:10.592248 INFO::Processing subtree level 2 2024-05-03 20:20:10.828152 INFO::Adjusting the last 1 batches sequentially 2024-05-03 20:20:10.840077 INFO::Done 2024-05-03 20:20:10.841524 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:10.853453 INFO::ASW Batch was 0.481404630927758 prior to batch effect correction and is now 0.481404630927758 . 2024-05-03 20:20:10.854385 INFO::ASW Label was 0.340534340573678 prior to batch effect correction and is now 0.340534340573678 . 2024-05-03 20:20:10.856254 INFO::Total function execution time is 0.480991125106812 s and adjustment time is 0.422205924987793 s ( 87.78 ) 2024-05-03 20:20:10.859099 INFO::Formatting Data. 2024-05-03 20:20:10.859847 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:10.861702 INFO::Removing potential empty rows and columns 2024-05-03 20:20:10.867071 INFO::Found 1000 missing values. 2024-05-03 20:20:10.892886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:10.893821 INFO::Done 2024-05-03 20:20:10.894816 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:10.902386 INFO::Starting hierarchical adjustment 2024-05-03 20:20:10.903779 INFO::Found 10 batches. 2024-05-03 20:20:11.931064 INFO::Set up parallel execution backend with 2 workers 2024-05-03 20:20:11.931975 INFO::Processing subtree level 1 with 10 batches using 2 cores. 2024-05-03 20:20:13.231136 INFO::Adjusting the last 2 batches sequentially 2024-05-03 20:20:13.232339 INFO::Adjusting sequential tree level 1 with 2 batches 2024-05-03 20:20:13.247282 INFO::Done 2024-05-03 20:20:13.247942 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:13.252676 INFO::ASW Batch was 0.481404630927758 prior to batch effect correction and is now 0.481404630927758 . 2024-05-03 20:20:13.253228 INFO::ASW Label was 0.340534340573678 prior to batch effect correction and is now 0.340534340573678 . 2024-05-03 20:20:13.253873 INFO::Total function execution time is 2.39496397972107 s and adjustment time is 2.34379887580872 s ( 97.86 ) 2024-05-03 20:20:13.500156 INFO::Formatting Data. 2024-05-03 20:20:13.501305 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:13.503225 INFO::Removing potential empty rows and columns 2024-05-03 20:20:13.505094 INFO::Found 0 missing values. 2024-05-03 20:20:13.509377 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:13.510058 INFO::Done 2024-05-03 20:20:13.510783 INFO::Acquiring quality metrics before batch effect correction. 2024-05-03 20:20:13.513871 INFO::Starting hierarchical adjustment 2024-05-03 20:20:13.514722 INFO::Found 3 batches. 2024-05-03 20:20:13.515237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used. 2024-05-03 20:20:13.516011 INFO::Using default BPPARAM 2024-05-03 20:20:13.516736 INFO::Processing subtree level 1 2024-05-03 20:20:13.677774 INFO::Adjusting the last 1 batches sequentially 2024-05-03 20:20:13.69461 INFO::Done 2024-05-03 20:20:13.695955 INFO::Acquiring quality metrics after batch effect correction. 2024-05-03 20:20:13.708478 INFO::ASW Batch was 0.211063784765991 prior to batch effect correction and is now -0.150788347352957 . 2024-05-03 20:20:13.710143 INFO::ASW Label was -0.176435083784057 prior to batch effect correction and is now 0.124291572773553 . 2024-05-03 20:20:13.712353 INFO::Total function execution time is 0.212270021438599 s and adjustment time is 0.18009090423584 s ( 84.84 ) 2024-05-03 20:20:13.905364 INFO::Formatting Data. 2024-05-03 20:20:13.906147 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:13.907915 INFO::Removing potential empty rows and columns 2024-05-03 20:20:13.90904 INFO::Found 2 missing values. 2024-05-03 20:20:13.911881 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:13.912608 INFO::Done 2024-05-03 20:20:13.96252 INFO::Found NA in Reference column 2024-05-03 20:20:13.979168 INFO::Require at least two references per batch. 2024-05-03 20:20:14.009987 INFO::Formatting Data. 2024-05-03 20:20:14.011049 INFO::Recognized SummarizedExperiment 2024-05-03 20:20:14.012018 INFO::Typecasting input to dataframe. 2024-05-03 20:20:14.024076 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.02573 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.030801 INFO::Found 0 missing values. 2024-05-03 20:20:14.040129 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.041052 INFO::Done 2024-05-03 20:20:14.057426 INFO::Formatting Data. 2024-05-03 20:20:14.05819 INFO::Recognized SummarizedExperiment 2024-05-03 20:20:14.059143 INFO::Typecasting input to dataframe. 2024-05-03 20:20:14.080209 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.081484 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.085302 INFO::Found 0 missing values. 2024-05-03 20:20:14.098588 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.09956 INFO::Done 2024-05-03 20:20:14.117924 INFO::Formatting Data. 2024-05-03 20:20:14.118639 INFO::Recognized SummarizedExperiment 2024-05-03 20:20:14.119144 INFO::Typecasting input to dataframe. 2024-05-03 20:20:14.137241 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.138814 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.140469 INFO::Found 0 missing values. 2024-05-03 20:20:14.141866 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. 2024-05-03 20:20:14.147948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.148851 INFO::Done 2024-05-03 20:20:14.165897 INFO::Formatting Data. 2024-05-03 20:20:14.166753 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.168174 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.169559 INFO::Found 0 missing values. 2024-05-03 20:20:14.173531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.174313 INFO::Done 2024-05-03 20:20:14.190509 INFO::Formatting Data. 2024-05-03 20:20:14.191594 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.19282 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.194281 INFO::Found 0 missing values. 2024-05-03 20:20:14.198149 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.19892 INFO::Done 2024-05-03 20:20:14.245999 INFO::Formatting Data. 2024-05-03 20:20:14.247103 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.248462 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.249934 INFO::Found 1 missing values. 2024-05-03 20:20:14.253213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.253713 INFO::Done 2024-05-03 20:20:14.281035 INFO::Formatting Data. 2024-05-03 20:20:14.2821 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.282993 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.284225 INFO::Found 2 missing values. 2024-05-03 20:20:14.285554 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. 2024-05-03 20:20:14.288849 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.289395 INFO::Done 2024-05-03 20:20:14.303816 INFO::Formatting Data. 2024-05-03 20:20:14.304837 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.305958 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.306908 INFO::Found 2 missing values. 2024-05-03 20:20:14.308404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.308915 INFO::Done 2024-05-03 20:20:14.326318 INFO::Formatting Data. 2024-05-03 20:20:14.327104 INFO::Typecasting input to dataframe. 2024-05-03 20:20:14.327894 INFO::Replacing NaNs with NAs. 2024-05-03 20:20:14.328738 INFO::Removing potential empty rows and columns 2024-05-03 20:20:14.329713 INFO::Found 0 missing values. 2024-05-03 20:20:14.333229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level. 2024-05-03 20:20:14.333733 INFO::Done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ] > > proc.time() user system elapsed 19.972 4.027 24.402
BERT.Rcheck/BERT-Ex.timings
name | user | system | elapsed | |
BERT | 27.551 | 1.633 | 19.820 | |
compute_asw | 0.025 | 0.002 | 0.027 | |
count_existing | 0.014 | 0.001 | 0.014 | |
generate_data_covariables | 0.017 | 0.001 | 0.018 | |
generate_dataset | 0.013 | 0.001 | 0.014 | |