Yannis Schumann
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:00 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 154/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the BERT package: - 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: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2024-05-12 06:18:22 -0400 (Sun, 12 May 2024) |
| EndedAt: 2024-05-12 06:19:42 -0400 (Sun, 12 May 2024) |
| EllapsedTime: 79.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
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###
### 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/BERT.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.0’
* 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 28.97 1.066 20.366
* 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-arm64/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 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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")
2024-05-12 06:19:22.093787 INFO::Formatting Data.
2024-05-12 06:19:22.098861 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:22.110759 INFO::Removing potential empty rows and columns
2024-05-12 06:19:22.420895 INFO::Found 0 missing values.
2024-05-12 06:19:22.425644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:22.42669 INFO::Done
2024-05-12 06:19:22.427466 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:22.447819 INFO::Starting hierarchical adjustment
2024-05-12 06:19:22.44901 INFO::Found 3 batches.
2024-05-12 06:19:22.449555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:22.450933 INFO::Using default BPPARAM
2024-05-12 06:19:22.451596 INFO::Processing subtree level 1
2024-05-12 06:19:22.58864 INFO::Adjusting the last 1 batches sequentially
2024-05-12 06:19:22.593655 INFO::Done
2024-05-12 06:19:22.594809 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:22.600223 INFO::ASW Batch was -0.0897391634619752 prior to batch effect correction and is now -0.0897391634619752 .
2024-05-12 06:19:22.601817 INFO::Total function execution time is 0.509596824645996 s and adjustment time is 0.144827127456665 s ( 28.42 )
2024-05-12 06:19:22.621556 INFO::Formatting Data.
2024-05-12 06:19:22.622511 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:22.623674 INFO::Removing potential empty rows and columns
2024-05-12 06:19:22.625075 INFO::Found 0 missing values.
2024-05-12 06:19:22.626238 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.
2024-05-12 06:19:22.640391 INFO::Formatting Data.
2024-05-12 06:19:22.641267 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:22.642217 INFO::Removing potential empty rows and columns
2024-05-12 06:19:22.643281 INFO::Found 0 missing values.
2024-05-12 06:19:22.644217 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.
2024-05-12 06:19:22.663415 INFO::Formatting Data.
2024-05-12 06:19:22.664251 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:22.665202 INFO::Removing potential empty rows and columns
2024-05-12 06:19:22.666216 INFO::Found 0 missing values.
2024-05-12 06:19:22.667073 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.
2024-05-12 06:19:22.67112 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:22.671745 INFO::Done
2024-05-12 06:19:22.672252 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:22.67433 INFO::Starting hierarchical adjustment
2024-05-12 06:19:22.675006 INFO::Found 2 batches.
2024-05-12 06:19:22.675505 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:22.676203 INFO::Using default BPPARAM
2024-05-12 06:19:22.67666 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:22.677497 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:22.704662 INFO::Done
2024-05-12 06:19:22.705435 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:22.707511 INFO::ASW Batch was 0.0226013988504001 prior to batch effect correction and is now -0.0659129518401254 .
2024-05-12 06:19:22.70829 INFO::Total function execution time is 0.045058012008667 s and adjustment time is 0.0297031402587891 s ( 65.92 )
2024-05-12 06:19:22.711353 INFO::Formatting Data.
2024-05-12 06:19:22.711938 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:22.721041 INFO::Formatting Data.
2024-05-12 06:19:22.7217 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:22.722497 INFO::Removing potential empty rows and columns
2024-05-12 06:19:22.723448 INFO::Found 0 missing values.
2024-05-12 06:19:22.72604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:22.726558 INFO::Done
2024-05-12 06:19:22.726997 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:22.729184 INFO::Starting hierarchical adjustment
2024-05-12 06:19:22.729818 INFO::Found 2 batches.
2024-05-12 06:19:22.730305 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:22.730871 INFO::Using default BPPARAM
2024-05-12 06:19:22.731299 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:22.732194 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:22.747302 INFO::Done
2024-05-12 06:19:22.747935 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:22.749855 INFO::ASW Batch was -0.056348916120393 prior to batch effect correction and is now -0.129232771173701 .
2024-05-12 06:19:22.750657 INFO::Total function execution time is 0.0296821594238281 s and adjustment time is 0.0175840854644775 s ( 59.24 )
2024-05-12 06:19:22.751612 INFO::Formatting Data.
2024-05-12 06:19:22.752142 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:22.752932 INFO::Removing potential empty rows and columns
2024-05-12 06:19:22.753905 INFO::Found 0 missing values.
2024-05-12 06:19:22.756533 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:22.757151 INFO::Done
2024-05-12 06:19:22.757623 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:22.759709 INFO::Starting hierarchical adjustment
2024-05-12 06:19:22.760425 INFO::Found 2 batches.
2024-05-12 06:19:22.760888 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:22.761546 INFO::Using default BPPARAM
2024-05-12 06:19:22.761998 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:22.762844 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:22.778621 INFO::Done
2024-05-12 06:19:22.77937 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:22.781433 INFO::ASW Batch was -0.056348916120393 prior to batch effect correction and is now -0.129232771173701 .
2024-05-12 06:19:22.782292 INFO::Total function execution time is 0.030623197555542 s and adjustment time is 0.0182979106903076 s ( 59.75 )
2024-05-12 06:19:25.378846 INFO::Formatting Data.
2024-05-12 06:19:25.379578 INFO::Recognized SummarizedExperiment
2024-05-12 06:19:25.380024 INFO::Typecasting input to dataframe.
2024-05-12 06:19:26.283017 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:26.284525 INFO::Removing potential empty rows and columns
2024-05-12 06:19:26.287831 INFO::Found 0 missing values.
2024-05-12 06:19:26.294131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:26.294825 INFO::Done
2024-05-12 06:19:26.295255 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:26.298932 INFO::Starting hierarchical adjustment
2024-05-12 06:19:26.299677 INFO::Found 2 batches.
2024-05-12 06:19:26.300078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:26.30118 INFO::Using default BPPARAM
2024-05-12 06:19:26.301637 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:26.30252 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:26.35563 INFO::Done
2024-05-12 06:19:26.356363 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:26.360085 INFO::ASW Batch was 0.0252473064299298 prior to batch effect correction and is now -0.104189042545522 .
2024-05-12 06:19:26.361064 INFO::Total function execution time is 0.982554912567139 s and adjustment time is 0.0560040473937988 s ( 5.7 )
2024-05-12 06:19:26.379221 INFO::Formatting Data.
2024-05-12 06:19:26.380076 INFO::Recognized SummarizedExperiment
2024-05-12 06:19:26.380533 INFO::Typecasting input to dataframe.
2024-05-12 06:19:26.389411 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:26.390617 INFO::Removing potential empty rows and columns
2024-05-12 06:19:26.393755 INFO::Found 0 missing values.
2024-05-12 06:19:26.399907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:26.400537 INFO::Done
2024-05-12 06:19:26.40097 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:26.405023 INFO::Starting hierarchical adjustment
2024-05-12 06:19:26.406014 INFO::Found 2 batches.
2024-05-12 06:19:26.406591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:26.407174 INFO::Using default BPPARAM
2024-05-12 06:19:26.407667 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:26.408861 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:26.435503 INFO::Done
2024-05-12 06:19:26.436461 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:26.440859 INFO::ASW Batch was 0.0035380080102202 prior to batch effect correction and is now 0.0035380080102202 .
2024-05-12 06:19:26.442026 INFO::Total function execution time is 0.0627791881561279 s and adjustment time is 0.0295898914337158 s ( 47.13 )
2024-05-12 06:19:26.464053 INFO::Formatting Data.
2024-05-12 06:19:26.464838 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:26.465639 INFO::Removing potential empty rows and columns
2024-05-12 06:19:26.466516 INFO::Found 0 missing values.
2024-05-12 06:19:26.46898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:26.469499 INFO::Done
2024-05-12 06:19:26.469915 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:26.471824 INFO::Starting hierarchical adjustment
2024-05-12 06:19:26.472481 INFO::Found 3 batches.
2024-05-12 06:19:26.472895 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:26.473373 INFO::Using default BPPARAM
2024-05-12 06:19:26.473797 INFO::Processing subtree level 1
2024-05-12 06:19:26.654953 INFO::Adjusting the last 1 batches sequentially
2024-05-12 06:19:26.65915 INFO::Done
2024-05-12 06:19:26.660213 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:26.66636 INFO::ASW Batch was -0.0600900552264547 prior to batch effect correction and is now -0.148248147535633 .
2024-05-12 06:19:26.667787 INFO::Total function execution time is 0.203794002532959 s and adjustment time is 0.186775922775269 s ( 91.65 )
2024-05-12 06:19:26.687775 INFO::Skipping initial DF formatting
2024-05-12 06:19:26.689355 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:26.693882 INFO::Starting hierarchical adjustment
2024-05-12 06:19:26.694894 INFO::Found 5 batches.
2024-05-12 06:19:26.695504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:26.696349 INFO::Using default BPPARAM
2024-05-12 06:19:26.69692 INFO::Processing subtree level 1
2024-05-12 06:19:26.857345 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:26.86353 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:26.902525 INFO::Done
2024-05-12 06:19:26.903559 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:26.910154 INFO::ASW Batch was 0.48987011330492 prior to batch effect correction and is now 0.48987011330492 .
2024-05-12 06:19:26.910998 INFO::ASW Label was 0.377694487568157 prior to batch effect correction and is now 0.377694487568157 .
2024-05-12 06:19:26.912393 INFO::Total function execution time is 0.224607944488525 s and adjustment time is 0.207736015319824 s ( 92.49 )
2024-05-12 06:19:26.935073 INFO::Formatting Data.
2024-05-12 06:19:26.935971 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:26.936927 INFO::Removing potential empty rows and columns
2024-05-12 06:19:26.938131 INFO::Found 0 missing values.
2024-05-12 06:19:26.941847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:26.942481 INFO::Done
2024-05-12 06:19:26.943015 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:26.946249 INFO::Starting hierarchical adjustment
2024-05-12 06:19:26.947096 INFO::Found 5 batches.
2024-05-12 06:19:26.947722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:26.948454 INFO::Using default BPPARAM
2024-05-12 06:19:26.948973 INFO::Processing subtree level 1
2024-05-12 06:19:27.096295 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.10069 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.125713 INFO::Done
2024-05-12 06:19:27.126857 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.13124 INFO::ASW Batch was 0.327302591423607 prior to batch effect correction and is now -0.0343120200172993 .
2024-05-12 06:19:27.131996 INFO::ASW Label was 0.471995817461456 prior to batch effect correction and is now 0.822746734968175 .
2024-05-12 06:19:27.134322 INFO::Total function execution time is 0.199100971221924 s and adjustment time is 0.178708791732788 s ( 89.76 )
2024-05-12 06:19:27.136116 INFO::Formatting Data.
2024-05-12 06:19:27.137343 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.138566 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.139927 INFO::Found 0 missing values.
2024-05-12 06:19:27.144873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.145994 INFO::Done
2024-05-12 06:19:27.146534 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.149748 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.150551 INFO::Found 5 batches.
2024-05-12 06:19:27.15101 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.151717 INFO::Using default BPPARAM
2024-05-12 06:19:27.152215 INFO::Processing subtree level 1
2024-05-12 06:19:27.271242 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.275153 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.297776 INFO::Done
2024-05-12 06:19:27.299001 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.303492 INFO::ASW Batch was 0.327302591423607 prior to batch effect correction and is now -0.0343120200172993 .
2024-05-12 06:19:27.304268 INFO::ASW Label was 0.471995817461456 prior to batch effect correction and is now 0.822746734968175 .
2024-05-12 06:19:27.30554 INFO::Total function execution time is 0.16948390007019 s and adjustment time is 0.147293090820312 s ( 86.91 )
2024-05-12 06:19:27.324335 INFO::Formatting Data.
2024-05-12 06:19:27.325246 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.326155 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.327775 INFO::Found 0 missing values.
2024-05-12 06:19:27.331446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.332054 INFO::Done
2024-05-12 06:19:27.332591 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.335796 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.3367 INFO::Found 5 batches.
2024-05-12 06:19:27.337253 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.337914 INFO::Using default BPPARAM
2024-05-12 06:19:27.338376 INFO::Processing subtree level 1
2024-05-12 06:19:27.453828 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.465725 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.491946 INFO::Done
2024-05-12 06:19:27.492722 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.496887 INFO::ASW Batch was 0.426485883924524 prior to batch effect correction and is now -0.0918171039523667 .
2024-05-12 06:19:27.497507 INFO::ASW Label was 0.364172810760507 prior to batch effect correction and is now 0.840124070354113 .
2024-05-12 06:19:27.498999 INFO::Total function execution time is 0.174778938293457 s and adjustment time is 0.155390024185181 s ( 88.91 )
2024-05-12 06:19:27.499784 INFO::Formatting Data.
2024-05-12 06:19:27.500316 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.501107 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.502391 INFO::Found 0 missing values.
2024-05-12 06:19:27.506052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.506581 INFO::Done
2024-05-12 06:19:27.507059 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.509807 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.510457 INFO::Found 5 batches.
2024-05-12 06:19:27.510926 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.511547 INFO::Using default BPPARAM
2024-05-12 06:19:27.511999 INFO::Processing subtree level 1
2024-05-12 06:19:27.626233 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.631945 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.656634 INFO::Done
2024-05-12 06:19:27.657902 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.662737 INFO::ASW Batch was 0.426485883924524 prior to batch effect correction and is now -0.0918171039523667 .
2024-05-12 06:19:27.663499 INFO::ASW Label was 0.364172810760507 prior to batch effect correction and is now 0.840124070354113 .
2024-05-12 06:19:27.66496 INFO::Total function execution time is 0.165030956268311 s and adjustment time is 0.146247863769531 s ( 88.62 )
2024-05-12 06:19:27.685647 INFO::Formatting Data.
2024-05-12 06:19:27.686573 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.6875 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.688566 INFO::Found 0 missing values.
2024-05-12 06:19:27.691479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.692055 INFO::Done
2024-05-12 06:19:27.692529 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.695453 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.696202 INFO::Found 2 batches.
2024-05-12 06:19:27.696663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.6973 INFO::Using default BPPARAM
2024-05-12 06:19:27.697744 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.698544 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.713789 INFO::Done
2024-05-12 06:19:27.714568 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.717616 INFO::ASW Batch was 0.451301657499124 prior to batch effect correction and is now -0.0244704775568572 .
2024-05-12 06:19:27.718237 INFO::ASW Label was 0.634665366092281 prior to batch effect correction and is now 0.929561182092748 .
2024-05-12 06:19:27.719036 INFO::Total function execution time is 0.0335550308227539 s and adjustment time is 0.017686128616333 s ( 52.71 )
2024-05-12 06:19:27.719747 INFO::Formatting Data.
2024-05-12 06:19:27.720277 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.721056 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.721969 INFO::Found 0 missing values.
2024-05-12 06:19:27.724432 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.724941 INFO::Done
2024-05-12 06:19:27.725388 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.728118 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.728817 INFO::Found 2 batches.
2024-05-12 06:19:27.729294 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.72986 INFO::Using default BPPARAM
2024-05-12 06:19:27.730307 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.731094 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.745722 INFO::Done
2024-05-12 06:19:27.746474 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.749397 INFO::ASW Batch was 0.451301657499124 prior to batch effect correction and is now -0.0244704775568572 .
2024-05-12 06:19:27.749966 INFO::ASW Label was 0.634665366092281 prior to batch effect correction and is now 0.929561182092748 .
2024-05-12 06:19:27.750688 INFO::Total function execution time is 0.0309309959411621 s and adjustment time is 0.0170109272003174 s ( 55 )
2024-05-12 06:19:27.763424 INFO::Formatting Data.
2024-05-12 06:19:27.764217 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.765176 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.76601 INFO::Found 0 missing values.
2024-05-12 06:19:27.767947 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.768456 INFO::Done
2024-05-12 06:19:27.768898 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.770789 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.771412 INFO::Found 2 batches.
2024-05-12 06:19:27.771859 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.772398 INFO::Using default BPPARAM
2024-05-12 06:19:27.772824 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.77357 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.805437 INFO::Done
2024-05-12 06:19:27.806215 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.80818 INFO::ASW Batch was 0.061467569777984 prior to batch effect correction and is now -0.129798279306482 .
2024-05-12 06:19:27.809006 INFO::Total function execution time is 0.0457351207733154 s and adjustment time is 0.0340960025787354 s ( 74.55 )
2024-05-12 06:19:27.821745 INFO::Formatting Data.
2024-05-12 06:19:27.822509 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.823339 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.824268 INFO::Found 0 missing values.
2024-05-12 06:19:27.825569 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.
2024-05-12 06:19:27.830059 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.830696 INFO::Done
2024-05-12 06:19:27.831169 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.834109 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.834864 INFO::Found 2 batches.
2024-05-12 06:19:27.83533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.835877 INFO::Using default BPPARAM
2024-05-12 06:19:27.836352 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.837249 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.854107 INFO::Done
2024-05-12 06:19:27.85484 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.857637 INFO::ASW Batch was 0.563653096671361 prior to batch effect correction and is now 0.0403637255975849 .
2024-05-12 06:19:27.858169 INFO::ASW Label was 0.535684790699992 prior to batch effect correction and is now 0.8930809396332 .
2024-05-12 06:19:27.858847 INFO::Total function execution time is 0.0372340679168701 s and adjustment time is 0.0193500518798828 s ( 51.97 )
2024-05-12 06:19:27.860112 INFO::Formatting Data.
2024-05-12 06:19:27.861581 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:27.862844 INFO::Removing potential empty rows and columns
2024-05-12 06:19:27.864788 INFO::Found 0 missing values.
2024-05-12 06:19:27.866474 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.
2024-05-12 06:19:27.871405 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:27.872037 INFO::Done
2024-05-12 06:19:27.872563 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:27.875205 INFO::Starting hierarchical adjustment
2024-05-12 06:19:27.875957 INFO::Found 2 batches.
2024-05-12 06:19:27.876462 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:27.877042 INFO::Using default BPPARAM
2024-05-12 06:19:27.877503 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:27.878411 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:27.895779 INFO::Done
2024-05-12 06:19:27.896514 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:27.899469 INFO::ASW Batch was 0.563653096671361 prior to batch effect correction and is now 0.0403637255975849 .
2024-05-12 06:19:27.900041 INFO::ASW Label was 0.535684790699992 prior to batch effect correction and is now 0.8930809396332 .
2024-05-12 06:19:27.900893 INFO::Total function execution time is 0.040755033493042 s and adjustment time is 0.019927978515625 s ( 48.9 )
2024-05-12 06:19:28.082676 INFO::Formatting Data.
2024-05-12 06:19:28.083502 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:28.084375 INFO::Removing potential empty rows and columns
2024-05-12 06:19:28.085356 INFO::Found 0 missing values.
2024-05-12 06:19:28.088042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:28.088571 INFO::Done
2024-05-12 06:19:28.089013 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:28.091163 INFO::Starting hierarchical adjustment
2024-05-12 06:19:28.091884 INFO::Found 3 batches.
2024-05-12 06:19:28.092358 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:28.092925 INFO::Using default BPPARAM
2024-05-12 06:19:28.093385 INFO::Processing subtree level 1
2024-05-12 06:19:28.177576 INFO::Adjusting the last 1 batches sequentially
2024-05-12 06:19:28.180528 INFO::Done
2024-05-12 06:19:28.181233 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:28.186082 INFO::ASW Batch was 0.023535336703191 prior to batch effect correction and is now 0.023535336703191 .
2024-05-12 06:19:28.187712 INFO::Total function execution time is 0.10490608215332 s and adjustment time is 0.0887999534606934 s ( 84.65 )
2024-05-12 06:19:28.191067 INFO::Formatting Data.
2024-05-12 06:19:28.192117 INFO::Typecasting input to dataframe.
2024-05-12 06:19:28.193374 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:28.194439 INFO::Removing potential empty rows and columns
2024-05-12 06:19:28.195683 INFO::Found 0 missing values.
2024-05-12 06:19:28.198805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:28.199661 INFO::Done
2024-05-12 06:19:28.200327 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:28.202561 INFO::Starting hierarchical adjustment
2024-05-12 06:19:28.203337 INFO::Found 3 batches.
2024-05-12 06:19:28.203799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:28.204819 INFO::Using default BPPARAM
2024-05-12 06:19:28.205268 INFO::Processing subtree level 1
2024-05-12 06:19:28.308737 INFO::Adjusting the last 1 batches sequentially
2024-05-12 06:19:28.311335 INFO::Done
2024-05-12 06:19:28.311778 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:28.316736 INFO::ASW Batch was 0.023535336703191 prior to batch effect correction and is now 0.023535336703191 .
2024-05-12 06:19:28.318102 INFO::Total function execution time is 0.127065896987915 s and adjustment time is 0.108065843582153 s ( 85.05 )
2024-05-12 06:19:28.327973 INFO::Formatting Data.
2024-05-12 06:19:28.328479 INFO::Typecasting input to dataframe.
2024-05-12 06:19:28.328836 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:28.329259 INFO::Removing potential empty rows and columns
2024-05-12 06:19:28.330368 INFO::Found 0 missing values.
2024-05-12 06:19:28.331609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:28.331855 INFO::Done
2024-05-12 06:19:28.33205 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:28.333932 INFO::Starting hierarchical adjustment
2024-05-12 06:19:28.334309 INFO::Found 3 batches.
2024-05-12 06:19:28.334577 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:28.334818 INFO::Using default BPPARAM
2024-05-12 06:19:28.335012 INFO::Processing subtree level 1
2024-05-12 06:19:28.375924 INFO::Adjusting the last 1 batches sequentially
2024-05-12 06:19:28.377243 INFO::Done
2024-05-12 06:19:28.377587 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:28.378877 INFO::ASW Batch was -0.0276245496027362 prior to batch effect correction and is now -0.0276245496027362 .
2024-05-12 06:19:28.379461 INFO::Total function execution time is 0.0516598224639893 s and adjustment time is 0.0430009365081787 s ( 83.24 )
2024-05-12 06:19:28.449576 INFO::Formatting Data.
2024-05-12 06:19:28.450143 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:28.450637 INFO::Removing potential empty rows and columns
2024-05-12 06:19:28.452056 INFO::Found 1000 missing values.
2024-05-12 06:19:28.45973 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:28.460098 INFO::Done
2024-05-12 06:19:28.460303 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:28.462763 INFO::Starting hierarchical adjustment
2024-05-12 06:19:28.463114 INFO::Found 10 batches.
2024-05-12 06:19:28.463323 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:28.463603 INFO::Using default BPPARAM
2024-05-12 06:19:28.463791 INFO::Processing subtree level 1
2024-05-12 06:19:28.569711 INFO::Processing subtree level 2
2024-05-12 06:19:28.677353 INFO::Adjusting the last 1 batches sequentially
2024-05-12 06:19:28.680121 INFO::Done
2024-05-12 06:19:28.680448 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:28.684249 INFO::ASW Batch was 0.540484115122637 prior to batch effect correction and is now 0.540484115122637 .
2024-05-12 06:19:28.684627 INFO::ASW Label was 0.278501728809254 prior to batch effect correction and is now 0.278501728809254 .
2024-05-12 06:19:28.685537 INFO::Total function execution time is 0.2359459400177 s and adjustment time is 0.217036008834839 s ( 91.99 )
2024-05-12 06:19:28.685989 INFO::Formatting Data.
2024-05-12 06:19:28.686343 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:28.68724 INFO::Removing potential empty rows and columns
2024-05-12 06:19:28.688968 INFO::Found 1000 missing values.
2024-05-12 06:19:28.696987 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:28.697546 INFO::Done
2024-05-12 06:19:28.697775 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:28.700746 INFO::Starting hierarchical adjustment
2024-05-12 06:19:28.70124 INFO::Found 10 batches.
2024-05-12 06:19:29.913871 INFO::Set up parallel execution backend with 2 workers
2024-05-12 06:19:29.91469 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-12 06:19:31.396886 INFO::Adjusting the last 2 batches sequentially
2024-05-12 06:19:31.400883 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-12 06:19:31.418167 INFO::Done
2024-05-12 06:19:31.418905 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:31.424576 INFO::ASW Batch was 0.540484115122637 prior to batch effect correction and is now 0.540484115122637 .
2024-05-12 06:19:31.425145 INFO::ASW Label was 0.278501728809254 prior to batch effect correction and is now 0.278501728809254 .
2024-05-12 06:19:31.42583 INFO::Total function execution time is 2.73978590965271 s and adjustment time is 2.71690917015076 s ( 99.17 )
2024-05-12 06:19:31.598964 INFO::Formatting Data.
2024-05-12 06:19:31.599828 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:31.600709 INFO::Removing potential empty rows and columns
2024-05-12 06:19:31.602533 INFO::Found 0 missing values.
2024-05-12 06:19:31.606076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:31.606641 INFO::Done
2024-05-12 06:19:31.607151 INFO::Acquiring quality metrics before batch effect correction.
2024-05-12 06:19:31.610521 INFO::Starting hierarchical adjustment
2024-05-12 06:19:31.611241 INFO::Found 3 batches.
2024-05-12 06:19:31.61172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-12 06:19:31.612805 INFO::Using default BPPARAM
2024-05-12 06:19:31.613293 INFO::Processing subtree level 1
2024-05-12 06:19:31.744126 INFO::Adjusting the last 1 batches sequentially
2024-05-12 06:19:31.748916 INFO::Done
2024-05-12 06:19:31.749488 INFO::Acquiring quality metrics after batch effect correction.
2024-05-12 06:19:31.75524 INFO::ASW Batch was 0.202223702776494 prior to batch effect correction and is now -0.144815958349583 .
2024-05-12 06:19:31.755846 INFO::ASW Label was -0.183249601666802 prior to batch effect correction and is now 0.0625470327223555 .
2024-05-12 06:19:31.757638 INFO::Total function execution time is 0.158804893493652 s and adjustment time is 0.137817144393921 s ( 86.78 )
2024-05-12 06:19:31.890556 INFO::Formatting Data.
2024-05-12 06:19:31.891444 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:31.892293 INFO::Removing potential empty rows and columns
2024-05-12 06:19:31.89372 INFO::Found 2 missing values.
2024-05-12 06:19:31.896274 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:31.896755 INFO::Done
2024-05-12 06:19:31.926048 INFO::Found NA in Reference column
2024-05-12 06:19:31.93667 INFO::Require at least two references per batch.
2024-05-12 06:19:31.958468 INFO::Formatting Data.
2024-05-12 06:19:31.959322 INFO::Recognized SummarizedExperiment
2024-05-12 06:19:31.959812 INFO::Typecasting input to dataframe.
2024-05-12 06:19:31.970816 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:31.972045 INFO::Removing potential empty rows and columns
2024-05-12 06:19:31.97572 INFO::Found 0 missing values.
2024-05-12 06:19:31.982604 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:31.983203 INFO::Done
2024-05-12 06:19:31.998449 INFO::Formatting Data.
2024-05-12 06:19:31.999264 INFO::Recognized SummarizedExperiment
2024-05-12 06:19:31.99973 INFO::Typecasting input to dataframe.
2024-05-12 06:19:32.016816 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.01822 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.022082 INFO::Found 0 missing values.
2024-05-12 06:19:32.033488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.03421 INFO::Done
2024-05-12 06:19:32.04958 INFO::Formatting Data.
2024-05-12 06:19:32.050399 INFO::Recognized SummarizedExperiment
2024-05-12 06:19:32.050904 INFO::Typecasting input to dataframe.
2024-05-12 06:19:32.066638 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.067743 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.068772 INFO::Found 0 missing values.
2024-05-12 06:19:32.069649 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.
2024-05-12 06:19:32.073844 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.074447 INFO::Done
2024-05-12 06:19:32.08603 INFO::Formatting Data.
2024-05-12 06:19:32.08684 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.087683 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.088681 INFO::Found 0 missing values.
2024-05-12 06:19:32.091851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.092374 INFO::Done
2024-05-12 06:19:32.10526 INFO::Formatting Data.
2024-05-12 06:19:32.106056 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.106867 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.107829 INFO::Found 0 missing values.
2024-05-12 06:19:32.110632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.111207 INFO::Done
2024-05-12 06:19:32.142946 INFO::Formatting Data.
2024-05-12 06:19:32.143846 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.144855 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.145993 INFO::Found 1 missing values.
2024-05-12 06:19:32.149168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.149686 INFO::Done
2024-05-12 06:19:32.170365 INFO::Formatting Data.
2024-05-12 06:19:32.171245 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.17208 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.173092 INFO::Found 2 missing values.
2024-05-12 06:19:32.174057 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.
2024-05-12 06:19:32.176339 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.176915 INFO::Done
2024-05-12 06:19:32.188896 INFO::Formatting Data.
2024-05-12 06:19:32.189781 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.190586 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.191609 INFO::Found 2 missing values.
2024-05-12 06:19:32.193208 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.193759 INFO::Done
2024-05-12 06:19:32.207038 INFO::Formatting Data.
2024-05-12 06:19:32.207978 INFO::Typecasting input to dataframe.
2024-05-12 06:19:32.208945 INFO::Replacing NaNs with NAs.
2024-05-12 06:19:32.210393 INFO::Removing potential empty rows and columns
2024-05-12 06:19:32.211736 INFO::Found 0 missing values.
2024-05-12 06:19:32.215328 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-12 06:19:32.215856 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.054 3.512 23.120
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.970 | 1.066 | 20.366 | |
| compute_asw | 0.029 | 0.002 | 0.031 | |
| count_existing | 0.015 | 0.002 | 0.017 | |
| generate_data_covariables | 0.013 | 0.002 | 0.016 | |
| generate_dataset | 0.013 | 0.002 | 0.015 | |