Yannis Schumann
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 154/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.0 |
| 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: 2024-06-10 12:39:30 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 12:40:36 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 66.0 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/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 21.22 0.853 15.596
* 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")
2024-06-10 12:40:17.051238 INFO::Formatting Data.
2024-06-10 12:40:17.053042 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:17.058171 INFO::Removing potential empty rows and columns
2024-06-10 12:40:17.246429 INFO::Found 0 missing values.
2024-06-10 12:40:17.249546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:17.250093 INFO::Done
2024-06-10 12:40:17.25057 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:17.263728 INFO::Starting hierarchical adjustment
2024-06-10 12:40:17.264502 INFO::Found 3 batches.
2024-06-10 12:40:17.264991 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:17.266 INFO::Using default BPPARAM
2024-06-10 12:40:17.266458 INFO::Processing subtree level 1
2024-06-10 12:40:17.362563 INFO::Adjusting the last 1 batches sequentially
2024-06-10 12:40:17.364569 INFO::Done
2024-06-10 12:40:17.365261 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:17.368086 INFO::ASW Batch was -0.0638933370846686 prior to batch effect correction and is now -0.0638933370846686 .
2024-06-10 12:40:17.369524 INFO::Total function execution time is 0.318646192550659 s and adjustment time is 0.100192070007324 s ( 31.44 )
2024-06-10 12:40:17.384843 INFO::Formatting Data.
2024-06-10 12:40:17.385567 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:17.38652 INFO::Removing potential empty rows and columns
2024-06-10 12:40:17.387639 INFO::Found 0 missing values.
2024-06-10 12:40:17.38858 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.
2024-06-10 12:40:17.399855 INFO::Formatting Data.
2024-06-10 12:40:17.400627 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:17.401494 INFO::Removing potential empty rows and columns
2024-06-10 12:40:17.402453 INFO::Found 0 missing values.
2024-06-10 12:40:17.403288 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.
2024-06-10 12:40:17.42002 INFO::Formatting Data.
2024-06-10 12:40:17.4207 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:17.421479 INFO::Removing potential empty rows and columns
2024-06-10 12:40:17.422431 INFO::Found 0 missing values.
2024-06-10 12:40:17.423245 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.
2024-06-10 12:40:17.427074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:17.427614 INFO::Done
2024-06-10 12:40:17.428106 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:17.429954 INFO::Starting hierarchical adjustment
2024-06-10 12:40:17.430585 INFO::Found 2 batches.
2024-06-10 12:40:17.431026 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:17.431599 INFO::Using default BPPARAM
2024-06-10 12:40:17.432029 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:17.432802 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:17.454756 INFO::Done
2024-06-10 12:40:17.455378 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:17.457171 INFO::ASW Batch was -0.0387308997576294 prior to batch effect correction and is now -0.121421162926697 .
2024-06-10 12:40:17.457921 INFO::Total function execution time is 0.0379810333251953 s and adjustment time is 0.0242621898651123 s ( 63.88 )
2024-06-10 12:40:17.460457 INFO::Formatting Data.
2024-06-10 12:40:17.461017 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:17.469783 INFO::Formatting Data.
2024-06-10 12:40:17.470444 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:17.471216 INFO::Removing potential empty rows and columns
2024-06-10 12:40:17.472204 INFO::Found 0 missing values.
2024-06-10 12:40:17.474687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:17.475192 INFO::Done
2024-06-10 12:40:17.475643 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:17.477539 INFO::Starting hierarchical adjustment
2024-06-10 12:40:17.478194 INFO::Found 2 batches.
2024-06-10 12:40:17.478646 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:17.479171 INFO::Using default BPPARAM
2024-06-10 12:40:17.479591 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:17.480343 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:17.494604 INFO::Done
2024-06-10 12:40:17.495181 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:17.496882 INFO::ASW Batch was 0.0562568028795991 prior to batch effect correction and is now -0.116041171055005 .
2024-06-10 12:40:17.497596 INFO::Total function execution time is 0.0278711318969727 s and adjustment time is 0.0165209770202637 s ( 59.28 )
2024-06-10 12:40:17.498512 INFO::Formatting Data.
2024-06-10 12:40:17.499015 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:17.499739 INFO::Removing potential empty rows and columns
2024-06-10 12:40:17.500652 INFO::Found 0 missing values.
2024-06-10 12:40:17.50301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:17.503471 INFO::Done
2024-06-10 12:40:17.503891 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:17.505606 INFO::Starting hierarchical adjustment
2024-06-10 12:40:17.506211 INFO::Found 2 batches.
2024-06-10 12:40:17.506643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:17.507152 INFO::Using default BPPARAM
2024-06-10 12:40:17.507573 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:17.508317 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:17.521604 INFO::Done
2024-06-10 12:40:17.522208 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:17.523407 INFO::ASW Batch was 0.0562568028795991 prior to batch effect correction and is now -0.116041171055005 .
2024-06-10 12:40:17.523809 INFO::Total function execution time is 0.0253589153289795 s and adjustment time is 0.0154960155487061 s ( 61.11 )
2024-06-10 12:40:19.571506 INFO::Formatting Data.
2024-06-10 12:40:19.571829 INFO::Recognized SummarizedExperiment
2024-06-10 12:40:19.572013 INFO::Typecasting input to dataframe.
2024-06-10 12:40:20.082668 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:20.083777 INFO::Removing potential empty rows and columns
2024-06-10 12:40:20.086681 INFO::Found 0 missing values.
2024-06-10 12:40:20.090895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:20.091327 INFO::Done
2024-06-10 12:40:20.091617 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:20.094736 INFO::Starting hierarchical adjustment
2024-06-10 12:40:20.09535 INFO::Found 2 batches.
2024-06-10 12:40:20.09575 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:20.096633 INFO::Using default BPPARAM
2024-06-10 12:40:20.097053 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:20.09784 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:20.143996 INFO::Done
2024-06-10 12:40:20.144737 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:20.148094 INFO::ASW Batch was -0.00805486115753264 prior to batch effect correction and is now -0.0935930236548541 .
2024-06-10 12:40:20.148894 INFO::Total function execution time is 0.577430963516235 s and adjustment time is 0.0487189292907715 s ( 8.44 )
2024-06-10 12:40:20.164822 INFO::Formatting Data.
2024-06-10 12:40:20.165571 INFO::Recognized SummarizedExperiment
2024-06-10 12:40:20.166006 INFO::Typecasting input to dataframe.
2024-06-10 12:40:20.173979 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:20.175061 INFO::Removing potential empty rows and columns
2024-06-10 12:40:20.178135 INFO::Found 0 missing values.
2024-06-10 12:40:20.183351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:20.183892 INFO::Done
2024-06-10 12:40:20.184226 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:20.186757 INFO::Starting hierarchical adjustment
2024-06-10 12:40:20.187239 INFO::Found 2 batches.
2024-06-10 12:40:20.187537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:20.187893 INFO::Using default BPPARAM
2024-06-10 12:40:20.188165 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:20.188743 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:20.202969 INFO::Done
2024-06-10 12:40:20.203464 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:20.205531 INFO::ASW Batch was -0.0176393094334106 prior to batch effect correction and is now -0.0176393094334106 .
2024-06-10 12:40:20.206032 INFO::Total function execution time is 0.0412929058074951 s and adjustment time is 0.0157701969146729 s ( 38.19 )
2024-06-10 12:40:20.21634 INFO::Formatting Data.
2024-06-10 12:40:20.216722 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:20.217068 INFO::Removing potential empty rows and columns
2024-06-10 12:40:20.21744 INFO::Found 0 missing values.
2024-06-10 12:40:20.218412 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:20.218599 INFO::Done
2024-06-10 12:40:20.21877 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:20.219516 INFO::Starting hierarchical adjustment
2024-06-10 12:40:20.219754 INFO::Found 3 batches.
2024-06-10 12:40:20.21992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:20.220121 INFO::Using default BPPARAM
2024-06-10 12:40:20.220282 INFO::Processing subtree level 1
2024-06-10 12:40:20.296549 INFO::Adjusting the last 1 batches sequentially
2024-06-10 12:40:20.298901 INFO::Done
2024-06-10 12:40:20.299551 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:20.302393 INFO::ASW Batch was -0.0906759928995696 prior to batch effect correction and is now -0.152137339180664 .
2024-06-10 12:40:20.303709 INFO::Total function execution time is 0.0871009826660156 s and adjustment time is 0.0791358947753906 s ( 90.86 )
2024-06-10 12:40:20.320837 INFO::Skipping initial DF formatting
2024-06-10 12:40:20.321215 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:20.323207 INFO::Starting hierarchical adjustment
2024-06-10 12:40:20.323601 INFO::Found 5 batches.
2024-06-10 12:40:20.323852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:20.324157 INFO::Using default BPPARAM
2024-06-10 12:40:20.324569 INFO::Processing subtree level 1
2024-06-10 12:40:20.446193 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:20.450401 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:20.481759 INFO::Done
2024-06-10 12:40:20.482725 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:20.489883 INFO::ASW Batch was 0.470678286565173 prior to batch effect correction and is now 0.470678286565173 .
2024-06-10 12:40:20.491064 INFO::ASW Label was 0.377158951627704 prior to batch effect correction and is now 0.377158951627704 .
2024-06-10 12:40:20.492467 INFO::Total function execution time is 0.171471118927002 s and adjustment time is 0.158083915710449 s ( 92.19 )
2024-06-10 12:40:20.514797 INFO::Formatting Data.
2024-06-10 12:40:20.51567 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:20.516606 INFO::Removing potential empty rows and columns
2024-06-10 12:40:20.517799 INFO::Found 0 missing values.
2024-06-10 12:40:20.521643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:20.522318 INFO::Done
2024-06-10 12:40:20.522844 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:20.525842 INFO::Starting hierarchical adjustment
2024-06-10 12:40:20.526571 INFO::Found 5 batches.
2024-06-10 12:40:20.527032 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:20.527664 INFO::Using default BPPARAM
2024-06-10 12:40:20.52814 INFO::Processing subtree level 1
2024-06-10 12:40:20.626153 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:20.628835 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:20.645288 INFO::Done
2024-06-10 12:40:20.645911 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:20.649025 INFO::ASW Batch was 0.302959663391332 prior to batch effect correction and is now -0.0596368566051541 .
2024-06-10 12:40:20.649588 INFO::ASW Label was 0.486145237758545 prior to batch effect correction and is now 0.801781406395496 .
2024-06-10 12:40:20.650472 INFO::Total function execution time is 0.135828018188477 s and adjustment time is 0.118849992752075 s ( 87.5 )
2024-06-10 12:40:20.651177 INFO::Formatting Data.
2024-06-10 12:40:20.65185 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:20.652744 INFO::Removing potential empty rows and columns
2024-06-10 12:40:20.653754 INFO::Found 0 missing values.
2024-06-10 12:40:20.65707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:20.65762 INFO::Done
2024-06-10 12:40:20.65806 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:20.660576 INFO::Starting hierarchical adjustment
2024-06-10 12:40:20.66126 INFO::Found 5 batches.
2024-06-10 12:40:20.661696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:20.662242 INFO::Using default BPPARAM
2024-06-10 12:40:20.662678 INFO::Processing subtree level 1
2024-06-10 12:40:20.76822 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:20.773196 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:20.79869 INFO::Done
2024-06-10 12:40:20.799806 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:20.804439 INFO::ASW Batch was 0.302959663391332 prior to batch effect correction and is now -0.0596368566051541 .
2024-06-10 12:40:20.805203 INFO::ASW Label was 0.486145237758545 prior to batch effect correction and is now 0.801781406395496 .
2024-06-10 12:40:20.806456 INFO::Total function execution time is 0.155173063278198 s and adjustment time is 0.137493133544922 s ( 88.61 )
2024-06-10 12:40:20.824305 INFO::Formatting Data.
2024-06-10 12:40:20.825194 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:20.826095 INFO::Removing potential empty rows and columns
2024-06-10 12:40:20.827102 INFO::Found 0 missing values.
2024-06-10 12:40:20.830763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:20.831329 INFO::Done
2024-06-10 12:40:20.831836 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:20.834669 INFO::Starting hierarchical adjustment
2024-06-10 12:40:20.835355 INFO::Found 5 batches.
2024-06-10 12:40:20.835858 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:20.836471 INFO::Using default BPPARAM
2024-06-10 12:40:20.836913 INFO::Processing subtree level 1
2024-06-10 12:40:20.966262 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:20.969692 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:20.991488 INFO::Done
2024-06-10 12:40:20.992325 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:20.996776 INFO::ASW Batch was 0.641122047432022 prior to batch effect correction and is now -0.10974624525985 .
2024-06-10 12:40:20.997515 INFO::ASW Label was 0.155105451813487 prior to batch effect correction and is now 0.831103023091263 .
2024-06-10 12:40:20.998832 INFO::Total function execution time is 0.174615859985352 s and adjustment time is 0.156203985214233 s ( 89.46 )
2024-06-10 12:40:20.999759 INFO::Formatting Data.
2024-06-10 12:40:21.000473 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.001417 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.002648 INFO::Found 0 missing values.
2024-06-10 12:40:21.006441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.007072 INFO::Done
2024-06-10 12:40:21.007553 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.01058 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.011368 INFO::Found 5 batches.
2024-06-10 12:40:21.011852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.012493 INFO::Using default BPPARAM
2024-06-10 12:40:21.013325 INFO::Processing subtree level 1
2024-06-10 12:40:21.137781 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:21.141827 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:21.162999 INFO::Done
2024-06-10 12:40:21.163839 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.167735 INFO::ASW Batch was 0.641122047432022 prior to batch effect correction and is now -0.10974624525985 .
2024-06-10 12:40:21.168468 INFO::ASW Label was 0.155105451813487 prior to batch effect correction and is now 0.831103023091263 .
2024-06-10 12:40:21.169796 INFO::Total function execution time is 0.169948101043701 s and adjustment time is 0.151722192764282 s ( 89.28 )
2024-06-10 12:40:21.188232 INFO::Formatting Data.
2024-06-10 12:40:21.189155 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.190075 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.191169 INFO::Found 0 missing values.
2024-06-10 12:40:21.193748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.194339 INFO::Done
2024-06-10 12:40:21.194795 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.19785 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.198548 INFO::Found 2 batches.
2024-06-10 12:40:21.199021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.199607 INFO::Using default BPPARAM
2024-06-10 12:40:21.200044 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:21.200846 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:21.21631 INFO::Done
2024-06-10 12:40:21.217565 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.220846 INFO::ASW Batch was 0.287258096024039 prior to batch effect correction and is now -0.0176581814274318 .
2024-06-10 12:40:21.22155 INFO::ASW Label was 0.737418234596593 prior to batch effect correction and is now 0.962276928603232 .
2024-06-10 12:40:21.222588 INFO::Total function execution time is 0.0344820022583008 s and adjustment time is 0.0178508758544922 s ( 51.77 )
2024-06-10 12:40:21.223531 INFO::Formatting Data.
2024-06-10 12:40:21.22413 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.225051 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.225991 INFO::Found 0 missing values.
2024-06-10 12:40:21.22851 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.229108 INFO::Done
2024-06-10 12:40:21.229557 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.232567 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.23336 INFO::Found 2 batches.
2024-06-10 12:40:21.233852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.234395 INFO::Using default BPPARAM
2024-06-10 12:40:21.234821 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:21.235652 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:21.250581 INFO::Done
2024-06-10 12:40:21.251362 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.25432 INFO::ASW Batch was 0.287258096024039 prior to batch effect correction and is now -0.0176581814274318 .
2024-06-10 12:40:21.254901 INFO::ASW Label was 0.737418234596593 prior to batch effect correction and is now 0.962276928603232 .
2024-06-10 12:40:21.255614 INFO::Total function execution time is 0.0320839881896973 s and adjustment time is 0.0173251628875732 s ( 54 )
2024-06-10 12:40:21.269119 INFO::Formatting Data.
2024-06-10 12:40:21.269954 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.270829 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.271676 INFO::Found 0 missing values.
2024-06-10 12:40:21.273636 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.274176 INFO::Done
2024-06-10 12:40:21.274646 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.276627 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.277309 INFO::Found 2 batches.
2024-06-10 12:40:21.277772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.278302 INFO::Using default BPPARAM
2024-06-10 12:40:21.278721 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:21.279509 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:21.312535 INFO::Done
2024-06-10 12:40:21.313323 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.315327 INFO::ASW Batch was 0.0125782643900685 prior to batch effect correction and is now -0.0906696321935014 .
2024-06-10 12:40:21.316152 INFO::Total function execution time is 0.0471880435943604 s and adjustment time is 0.0352909564971924 s ( 74.79 )
2024-06-10 12:40:21.329442 INFO::Formatting Data.
2024-06-10 12:40:21.330222 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.331081 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.331996 INFO::Found 0 missing values.
2024-06-10 12:40:21.333285 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.
2024-06-10 12:40:21.33731 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.337888 INFO::Done
2024-06-10 12:40:21.338327 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.341169 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.341967 INFO::Found 2 batches.
2024-06-10 12:40:21.342451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.342999 INFO::Using default BPPARAM
2024-06-10 12:40:21.343462 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:21.344504 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:21.360969 INFO::Done
2024-06-10 12:40:21.361728 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.364571 INFO::ASW Batch was 0.431295212134484 prior to batch effect correction and is now 0.0676704310899217 .
2024-06-10 12:40:21.365146 INFO::ASW Label was 0.647991142404623 prior to batch effect correction and is now 0.87998842787033 .
2024-06-10 12:40:21.365854 INFO::Total function execution time is 0.0365469455718994 s and adjustment time is 0.0190920829772949 s ( 52.24 )
2024-06-10 12:40:21.36652 INFO::Formatting Data.
2024-06-10 12:40:21.367034 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.367906 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.368873 INFO::Found 0 missing values.
2024-06-10 12:40:21.369712 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.
2024-06-10 12:40:21.373865 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.374476 INFO::Done
2024-06-10 12:40:21.374977 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.377829 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.378586 INFO::Found 2 batches.
2024-06-10 12:40:21.379064 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.379608 INFO::Using default BPPARAM
2024-06-10 12:40:21.380044 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:21.380952 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:21.39711 INFO::Done
2024-06-10 12:40:21.397805 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.400639 INFO::ASW Batch was 0.431295212134484 prior to batch effect correction and is now 0.0676704310899217 .
2024-06-10 12:40:21.401308 INFO::ASW Label was 0.647991142404623 prior to batch effect correction and is now 0.87998842787033 .
2024-06-10 12:40:21.402006 INFO::Total function execution time is 0.0354790687561035 s and adjustment time is 0.0186479091644287 s ( 52.56 )
2024-06-10 12:40:21.620898 INFO::Formatting Data.
2024-06-10 12:40:21.621733 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.622559 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.623555 INFO::Found 0 missing values.
2024-06-10 12:40:21.626184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.626677 INFO::Done
2024-06-10 12:40:21.627127 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.62902 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.629632 INFO::Found 3 batches.
2024-06-10 12:40:21.630138 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.630654 INFO::Using default BPPARAM
2024-06-10 12:40:21.631086 INFO::Processing subtree level 1
2024-06-10 12:40:21.738767 INFO::Adjusting the last 1 batches sequentially
2024-06-10 12:40:21.743765 INFO::Done
2024-06-10 12:40:21.744354 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.749941 INFO::ASW Batch was -0.0544213943140797 prior to batch effect correction and is now -0.0544213943140797 .
2024-06-10 12:40:21.751408 INFO::Total function execution time is 0.130573034286499 s and adjustment time is 0.114235877990723 s ( 87.49 )
2024-06-10 12:40:21.752738 INFO::Formatting Data.
2024-06-10 12:40:21.753823 INFO::Typecasting input to dataframe.
2024-06-10 12:40:21.754501 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.755354 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.756411 INFO::Found 0 missing values.
2024-06-10 12:40:21.759148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.759698 INFO::Done
2024-06-10 12:40:21.7602 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.762123 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.763103 INFO::Found 3 batches.
2024-06-10 12:40:21.763564 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.764512 INFO::Using default BPPARAM
2024-06-10 12:40:21.765047 INFO::Processing subtree level 1
2024-06-10 12:40:21.871273 INFO::Adjusting the last 1 batches sequentially
2024-06-10 12:40:21.876427 INFO::Done
2024-06-10 12:40:21.877034 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:21.883171 INFO::ASW Batch was -0.0544213943140797 prior to batch effect correction and is now -0.0544213943140797 .
2024-06-10 12:40:21.884655 INFO::Total function execution time is 0.132179975509644 s and adjustment time is 0.113771200180054 s ( 86.07 )
2024-06-10 12:40:21.902978 INFO::Formatting Data.
2024-06-10 12:40:21.903901 INFO::Typecasting input to dataframe.
2024-06-10 12:40:21.90475 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:21.905718 INFO::Removing potential empty rows and columns
2024-06-10 12:40:21.90736 INFO::Found 0 missing values.
2024-06-10 12:40:21.910486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:21.911171 INFO::Done
2024-06-10 12:40:21.911664 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:21.913813 INFO::Starting hierarchical adjustment
2024-06-10 12:40:21.914571 INFO::Found 3 batches.
2024-06-10 12:40:21.915079 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:21.916383 INFO::Using default BPPARAM
2024-06-10 12:40:21.916899 INFO::Processing subtree level 1
2024-06-10 12:40:22.030455 INFO::Adjusting the last 1 batches sequentially
2024-06-10 12:40:22.035326 INFO::Done
2024-06-10 12:40:22.036081 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:22.042145 INFO::ASW Batch was -0.0731856669604909 prior to batch effect correction and is now -0.0731856669604909 .
2024-06-10 12:40:22.043685 INFO::Total function execution time is 0.140787124633789 s and adjustment time is 0.120875120162964 s ( 85.86 )
2024-06-10 12:40:22.234272 INFO::Formatting Data.
2024-06-10 12:40:22.23526 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:22.236475 INFO::Removing potential empty rows and columns
2024-06-10 12:40:22.239368 INFO::Found 1000 missing values.
2024-06-10 12:40:22.257781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:22.258691 INFO::Done
2024-06-10 12:40:22.259361 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:22.265997 INFO::Starting hierarchical adjustment
2024-06-10 12:40:22.267001 INFO::Found 10 batches.
2024-06-10 12:40:22.267584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:22.26827 INFO::Using default BPPARAM
2024-06-10 12:40:22.268784 INFO::Processing subtree level 1
2024-06-10 12:40:22.408049 INFO::Processing subtree level 2
2024-06-10 12:40:22.588877 INFO::Adjusting the last 1 batches sequentially
2024-06-10 12:40:22.593308 INFO::Done
2024-06-10 12:40:22.593913 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:22.600717 INFO::ASW Batch was 0.476169228197568 prior to batch effect correction and is now 0.476169228197568 .
2024-06-10 12:40:22.601387 INFO::ASW Label was 0.311360824144789 prior to batch effect correction and is now 0.311360824144789 .
2024-06-10 12:40:22.603151 INFO::Total function execution time is 0.368669033050537 s and adjustment time is 0.326512813568115 s ( 88.57 )
2024-06-10 12:40:22.60399 INFO::Formatting Data.
2024-06-10 12:40:22.604558 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:22.605657 INFO::Removing potential empty rows and columns
2024-06-10 12:40:22.608791 INFO::Found 1000 missing values.
2024-06-10 12:40:22.626247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:22.627092 INFO::Done
2024-06-10 12:40:22.6276 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:22.633557 INFO::Starting hierarchical adjustment
2024-06-10 12:40:22.634353 INFO::Found 10 batches.
2024-06-10 12:40:23.818791 INFO::Set up parallel execution backend with 2 workers
2024-06-10 12:40:23.81969 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-10 12:40:25.131081 INFO::Adjusting the last 2 batches sequentially
2024-06-10 12:40:25.132662 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 12:40:25.149262 INFO::Done
2024-06-10 12:40:25.149964 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:25.156278 INFO::ASW Batch was 0.476169228197568 prior to batch effect correction and is now 0.476169228197568 .
2024-06-10 12:40:25.156974 INFO::ASW Label was 0.311360824144789 prior to batch effect correction and is now 0.311360824144789 .
2024-06-10 12:40:25.15777 INFO::Total function execution time is 2.55377197265625 s and adjustment time is 2.5150351524353 s ( 98.48 )
2024-06-10 12:40:25.359367 INFO::Formatting Data.
2024-06-10 12:40:25.36046 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:25.36162 INFO::Removing potential empty rows and columns
2024-06-10 12:40:25.363006 INFO::Found 0 missing values.
2024-06-10 12:40:25.36772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:25.368689 INFO::Done
2024-06-10 12:40:25.369347 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 12:40:25.373028 INFO::Starting hierarchical adjustment
2024-06-10 12:40:25.373908 INFO::Found 3 batches.
2024-06-10 12:40:25.374526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 12:40:25.375401 INFO::Using default BPPARAM
2024-06-10 12:40:25.376002 INFO::Processing subtree level 1
2024-06-10 12:40:25.531787 INFO::Adjusting the last 1 batches sequentially
2024-06-10 12:40:25.539834 INFO::Done
2024-06-10 12:40:25.540634 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 12:40:25.549796 INFO::ASW Batch was 0.205893661871059 prior to batch effect correction and is now -0.1286544841325 .
2024-06-10 12:40:25.550697 INFO::ASW Label was -0.212191800404033 prior to batch effect correction and is now -0.102758237331861 .
2024-06-10 12:40:25.552432 INFO::Total function execution time is 0.19314694404602 s and adjustment time is 0.166041135787964 s ( 85.97 )
2024-06-10 12:40:25.755541 INFO::Formatting Data.
2024-06-10 12:40:25.756719 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:25.757913 INFO::Removing potential empty rows and columns
2024-06-10 12:40:25.759368 INFO::Found 2 missing values.
2024-06-10 12:40:25.763121 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:25.763876 INFO::Done
2024-06-10 12:40:25.804512 INFO::Found NA in Reference column
2024-06-10 12:40:25.818955 INFO::Require at least two references per batch.
2024-06-10 12:40:25.847979 INFO::Formatting Data.
2024-06-10 12:40:25.848976 INFO::Recognized SummarizedExperiment
2024-06-10 12:40:25.849546 INFO::Typecasting input to dataframe.
2024-06-10 12:40:25.863291 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:25.864813 INFO::Removing potential empty rows and columns
2024-06-10 12:40:25.869323 INFO::Found 0 missing values.
2024-06-10 12:40:25.877478 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:25.878197 INFO::Done
2024-06-10 12:40:25.896928 INFO::Formatting Data.
2024-06-10 12:40:25.897951 INFO::Recognized SummarizedExperiment
2024-06-10 12:40:25.898511 INFO::Typecasting input to dataframe.
2024-06-10 12:40:25.918731 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:25.920208 INFO::Removing potential empty rows and columns
2024-06-10 12:40:25.924463 INFO::Found 0 missing values.
2024-06-10 12:40:25.938416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:25.939341 INFO::Done
2024-06-10 12:40:25.95799 INFO::Formatting Data.
2024-06-10 12:40:25.958971 INFO::Recognized SummarizedExperiment
2024-06-10 12:40:25.959559 INFO::Typecasting input to dataframe.
2024-06-10 12:40:25.979397 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:25.980551 INFO::Removing potential empty rows and columns
2024-06-10 12:40:25.981608 INFO::Found 0 missing values.
2024-06-10 12:40:25.983408 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.
2024-06-10 12:40:25.988744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:25.989614 INFO::Done
2024-06-10 12:40:26.004304 INFO::Formatting Data.
2024-06-10 12:40:26.005364 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:26.006412 INFO::Removing potential empty rows and columns
2024-06-10 12:40:26.00753 INFO::Found 0 missing values.
2024-06-10 12:40:26.010543 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:26.01121 INFO::Done
2024-06-10 12:40:26.027316 INFO::Formatting Data.
2024-06-10 12:40:26.028395 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:26.029615 INFO::Removing potential empty rows and columns
2024-06-10 12:40:26.030801 INFO::Found 0 missing values.
2024-06-10 12:40:26.034245 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:26.035035 INFO::Done
2024-06-10 12:40:26.082539 INFO::Formatting Data.
2024-06-10 12:40:26.083839 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:26.085061 INFO::Removing potential empty rows and columns
2024-06-10 12:40:26.086643 INFO::Found 1 missing values.
2024-06-10 12:40:26.091073 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:26.091794 INFO::Done
2024-06-10 12:40:26.116761 INFO::Formatting Data.
2024-06-10 12:40:26.117786 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:26.118721 INFO::Removing potential empty rows and columns
2024-06-10 12:40:26.119795 INFO::Found 2 missing values.
2024-06-10 12:40:26.120865 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.
2024-06-10 12:40:26.123851 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:26.124749 INFO::Done
2024-06-10 12:40:26.14048 INFO::Formatting Data.
2024-06-10 12:40:26.141659 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:26.142881 INFO::Removing potential empty rows and columns
2024-06-10 12:40:26.144238 INFO::Found 2 missing values.
2024-06-10 12:40:26.146477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:26.147231 INFO::Done
2024-06-10 12:40:26.164026 INFO::Formatting Data.
2024-06-10 12:40:26.165098 INFO::Typecasting input to dataframe.
2024-06-10 12:40:26.166109 INFO::Replacing NaNs with NAs.
2024-06-10 12:40:26.16757 INFO::Removing potential empty rows and columns
2024-06-10 12:40:26.169165 INFO::Found 0 missing values.
2024-06-10 12:40:26.174228 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 12:40:26.17483 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
15.139 2.992 18.284
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 21.220 | 0.853 | 15.596 | |
| compute_asw | 0.014 | 0.000 | 0.016 | |
| count_existing | 0.006 | 0.000 | 0.006 | |
| generate_data_covariables | 0.005 | 0.000 | 0.005 | |
| generate_dataset | 0.005 | 0.000 | 0.005 | |