Yannis Schumann
| Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:05 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-07-22 01:11:09 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 01:13:49 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 159.7 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 45.588 2.77 40.957
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-07-22 01:13:09.738721 INFO::Formatting Data.
2024-07-22 01:13:09.748455 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:09.783443 INFO::Removing potential empty rows and columns
2024-07-22 01:13:10.613992 INFO::Found 0 missing values.
2024-07-22 01:13:10.626361 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:10.627836 INFO::Done
2024-07-22 01:13:10.632099 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:10.668759 INFO::Starting hierarchical adjustment
2024-07-22 01:13:10.670579 INFO::Found 3 batches.
2024-07-22 01:13:10.671838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:10.677184 INFO::Using default BPPARAM
2024-07-22 01:13:10.678737 INFO::Processing subtree level 1
2024-07-22 01:13:10.971444 INFO::Adjusting the last 1 batches sequentially
2024-07-22 01:13:10.977599 INFO::Done
2024-07-22 01:13:10.979089 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:10.985336 INFO::ASW Batch was -0.00310675353006635 prior to batch effect correction and is now -0.00310675353006635 .
2024-07-22 01:13:10.987881 INFO::Total function execution time is 1.25007796287537 s and adjustment time is 0.307340145111084 s ( 24.59 )
2024-07-22 01:13:11.02445 INFO::Formatting Data.
2024-07-22 01:13:11.02596 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:11.028409 INFO::Removing potential empty rows and columns
2024-07-22 01:13:11.031485 INFO::Found 0 missing values.
2024-07-22 01:13:11.034056 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.
2024-07-22 01:13:11.064012 INFO::Formatting Data.
2024-07-22 01:13:11.068575 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:11.070925 INFO::Removing potential empty rows and columns
2024-07-22 01:13:11.073668 INFO::Found 0 missing values.
2024-07-22 01:13:11.076048 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.
2024-07-22 01:13:11.130994 INFO::Formatting Data.
2024-07-22 01:13:11.132541 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:11.134605 INFO::Removing potential empty rows and columns
2024-07-22 01:13:11.137303 INFO::Found 0 missing values.
2024-07-22 01:13:11.13976 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.
2024-07-22 01:13:11.152015 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:11.153482 INFO::Done
2024-07-22 01:13:11.154829 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:11.161539 INFO::Starting hierarchical adjustment
2024-07-22 01:13:11.163436 INFO::Found 2 batches.
2024-07-22 01:13:11.164809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:11.166719 INFO::Using default BPPARAM
2024-07-22 01:13:11.169863 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:11.173109 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:11.242234 INFO::Done
2024-07-22 01:13:11.243723 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:11.248397 INFO::ASW Batch was 0.0334170223160147 prior to batch effect correction and is now -0.0883301026173766 .
2024-07-22 01:13:11.250502 INFO::Total function execution time is 0.119542837142944 s and adjustment time is 0.0791518688201904 s ( 66.21 )
2024-07-22 01:13:11.255932 INFO::Formatting Data.
2024-07-22 01:13:11.25734 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:11.28705 INFO::Formatting Data.
2024-07-22 01:13:11.28866 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:11.29078 INFO::Removing potential empty rows and columns
2024-07-22 01:13:11.293272 INFO::Found 0 missing values.
2024-07-22 01:13:11.305628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:11.306985 INFO::Done
2024-07-22 01:13:11.308174 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:11.315085 INFO::Starting hierarchical adjustment
2024-07-22 01:13:11.316884 INFO::Found 2 batches.
2024-07-22 01:13:11.318127 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:11.319513 INFO::Using default BPPARAM
2024-07-22 01:13:11.322424 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:11.324914 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:11.371471 INFO::Done
2024-07-22 01:13:11.37349 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:11.379002 INFO::ASW Batch was -0.0463326010532855 prior to batch effect correction and is now -0.115592129259393 .
2024-07-22 01:13:11.380977 INFO::Total function execution time is 0.0939719676971436 s and adjustment time is 0.054940938949585 s ( 58.47 )
2024-07-22 01:13:11.383566 INFO::Formatting Data.
2024-07-22 01:13:11.385049 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:11.38716 INFO::Removing potential empty rows and columns
2024-07-22 01:13:11.389806 INFO::Found 0 missing values.
2024-07-22 01:13:11.401817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:11.403353 INFO::Done
2024-07-22 01:13:11.406232 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:11.410569 INFO::Starting hierarchical adjustment
2024-07-22 01:13:11.412346 INFO::Found 2 batches.
2024-07-22 01:13:11.413402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:11.414633 INFO::Using default BPPARAM
2024-07-22 01:13:11.415696 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:11.419293 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:11.465858 INFO::Done
2024-07-22 01:13:11.467183 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:11.471609 INFO::ASW Batch was -0.0463326010532855 prior to batch effect correction and is now -0.115592129259393 .
2024-07-22 01:13:11.473373 INFO::Total function execution time is 0.0898439884185791 s and adjustment time is 0.0538060665130615 s ( 59.89 )
2024-07-22 01:13:17.867046 INFO::Formatting Data.
2024-07-22 01:13:17.868347 INFO::Recognized SummarizedExperiment
2024-07-22 01:13:17.869385 INFO::Typecasting input to dataframe.
2024-07-22 01:13:19.117183 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:19.119509 INFO::Removing potential empty rows and columns
2024-07-22 01:13:19.129955 INFO::Found 0 missing values.
2024-07-22 01:13:19.153794 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:19.155052 INFO::Done
2024-07-22 01:13:19.156126 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:19.166148 INFO::Starting hierarchical adjustment
2024-07-22 01:13:19.167763 INFO::Found 2 batches.
2024-07-22 01:13:19.168842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:19.170882 INFO::Using default BPPARAM
2024-07-22 01:13:19.171994 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:19.175238 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:19.330069 INFO::Done
2024-07-22 01:13:19.333426 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:19.342603 INFO::ASW Batch was 0.00479084532904998 prior to batch effect correction and is now -0.09818340025616 .
2024-07-22 01:13:19.346244 INFO::Total function execution time is 1.47999286651611 s and adjustment time is 0.162603855133057 s ( 10.99 )
2024-07-22 01:13:19.400091 INFO::Formatting Data.
2024-07-22 01:13:19.401476 INFO::Recognized SummarizedExperiment
2024-07-22 01:13:19.402891 INFO::Typecasting input to dataframe.
2024-07-22 01:13:19.432751 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:19.434843 INFO::Removing potential empty rows and columns
2024-07-22 01:13:19.445939 INFO::Found 0 missing values.
2024-07-22 01:13:19.466855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:19.468042 INFO::Done
2024-07-22 01:13:19.469024 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:19.477211 INFO::Starting hierarchical adjustment
2024-07-22 01:13:19.479208 INFO::Found 2 batches.
2024-07-22 01:13:19.480494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:19.481869 INFO::Using default BPPARAM
2024-07-22 01:13:19.48296 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:19.484965 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:19.561828 INFO::Done
2024-07-22 01:13:19.563119 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:19.574555 INFO::ASW Batch was -0.00300987152293676 prior to batch effect correction and is now -0.00300987152293676 .
2024-07-22 01:13:19.576295 INFO::Total function execution time is 0.17618203163147 s and adjustment time is 0.0829989910125732 s ( 47.11 )
2024-07-22 01:13:19.62795 INFO::Formatting Data.
2024-07-22 01:13:19.631891 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:19.633766 INFO::Removing potential empty rows and columns
2024-07-22 01:13:19.635972 INFO::Found 0 missing values.
2024-07-22 01:13:19.643722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:19.64503 INFO::Done
2024-07-22 01:13:19.646163 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:19.649845 INFO::Starting hierarchical adjustment
2024-07-22 01:13:19.651273 INFO::Found 3 batches.
2024-07-22 01:13:19.654459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:19.655683 INFO::Using default BPPARAM
2024-07-22 01:13:19.656786 INFO::Processing subtree level 1
2024-07-22 01:13:20.120603 INFO::Adjusting the last 1 batches sequentially
2024-07-22 01:13:20.131694 INFO::Done
2024-07-22 01:13:20.13465 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:20.145698 INFO::ASW Batch was 0.015508537906138 prior to batch effect correction and is now -0.190146487503768 .
2024-07-22 01:13:20.14937 INFO::Total function execution time is 0.520480871200562 s and adjustment time is 0.480628967285156 s ( 92.34 )
2024-07-22 01:13:20.188707 INFO::Skipping initial DF formatting
2024-07-22 01:13:20.190114 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:20.200315 INFO::Starting hierarchical adjustment
2024-07-22 01:13:20.202208 INFO::Found 5 batches.
2024-07-22 01:13:20.203517 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:20.205233 INFO::Using default BPPARAM
2024-07-22 01:13:20.206699 INFO::Processing subtree level 1
2024-07-22 01:13:20.590894 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:20.603404 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:20.683571 INFO::Done
2024-07-22 01:13:20.685172 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:20.697383 INFO::ASW Batch was 0.499502338234185 prior to batch effect correction and is now 0.499502338234185 .
2024-07-22 01:13:20.699015 INFO::ASW Label was 0.413815675928221 prior to batch effect correction and is now 0.413815675928221 .
2024-07-22 01:13:20.701515 INFO::Total function execution time is 0.512727022171021 s and adjustment time is 0.481695890426636 s ( 93.95 )
2024-07-22 01:13:20.764371 INFO::Formatting Data.
2024-07-22 01:13:20.766144 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:20.768643 INFO::Removing potential empty rows and columns
2024-07-22 01:13:20.771583 INFO::Found 0 missing values.
2024-07-22 01:13:20.78334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:20.784792 INFO::Done
2024-07-22 01:13:20.786048 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:20.793235 INFO::Starting hierarchical adjustment
2024-07-22 01:13:20.795185 INFO::Found 5 batches.
2024-07-22 01:13:20.796637 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:20.798192 INFO::Using default BPPARAM
2024-07-22 01:13:20.799471 INFO::Processing subtree level 1
2024-07-22 01:13:21.071567 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:21.084507 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:21.147244 INFO::Done
2024-07-22 01:13:21.148639 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:21.156749 INFO::ASW Batch was 0.439248409227487 prior to batch effect correction and is now -0.0255832327945854 .
2024-07-22 01:13:21.159067 INFO::ASW Label was 0.315251830909019 prior to batch effect correction and is now 0.787453991761292 .
2024-07-22 01:13:21.161956 INFO::Total function execution time is 0.396811962127686 s and adjustment time is 0.352486133575439 s ( 88.83 )
2024-07-22 01:13:21.164261 INFO::Formatting Data.
2024-07-22 01:13:21.165887 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:21.168062 INFO::Removing potential empty rows and columns
2024-07-22 01:13:21.170598 INFO::Found 0 missing values.
2024-07-22 01:13:21.182057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:21.183513 INFO::Done
2024-07-22 01:13:21.184878 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:21.192095 INFO::Starting hierarchical adjustment
2024-07-22 01:13:21.193967 INFO::Found 5 batches.
2024-07-22 01:13:21.195509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:21.197235 INFO::Using default BPPARAM
2024-07-22 01:13:21.199133 INFO::Processing subtree level 1
2024-07-22 01:13:21.467629 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:21.480828 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:21.541948 INFO::Done
2024-07-22 01:13:21.543483 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:21.551467 INFO::ASW Batch was 0.439248409227487 prior to batch effect correction and is now -0.0255832327945854 .
2024-07-22 01:13:21.553061 INFO::ASW Label was 0.315251830909019 prior to batch effect correction and is now 0.787453991761292 .
2024-07-22 01:13:21.556029 INFO::Total function execution time is 0.391179084777832 s and adjustment time is 0.348294019699097 s ( 89.04 )
2024-07-22 01:13:21.594614 INFO::Formatting Data.
2024-07-22 01:13:21.598722 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:21.601394 INFO::Removing potential empty rows and columns
2024-07-22 01:13:21.604321 INFO::Found 0 missing values.
2024-07-22 01:13:21.622819 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:21.625478 INFO::Done
2024-07-22 01:13:21.627137 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:21.634608 INFO::Starting hierarchical adjustment
2024-07-22 01:13:21.638333 INFO::Found 5 batches.
2024-07-22 01:13:21.63993 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:21.641669 INFO::Using default BPPARAM
2024-07-22 01:13:21.643501 INFO::Processing subtree level 1
2024-07-22 01:13:21.89843 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:21.910214 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:21.97125 INFO::Done
2024-07-22 01:13:21.972851 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:21.980735 INFO::ASW Batch was 0.135920191887013 prior to batch effect correction and is now -0.0747912484637752 .
2024-07-22 01:13:21.982248 INFO::ASW Label was 0.567691681686271 prior to batch effect correction and is now 0.839290607470238 .
2024-07-22 01:13:21.986356 INFO::Total function execution time is 0.390569925308228 s and adjustment time is 0.333513021469116 s ( 85.39 )
2024-07-22 01:13:21.988973 INFO::Formatting Data.
2024-07-22 01:13:21.992991 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:21.996134 INFO::Removing potential empty rows and columns
2024-07-22 01:13:22.001347 INFO::Found 0 missing values.
2024-07-22 01:13:22.01532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:22.016788 INFO::Done
2024-07-22 01:13:22.018029 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:22.024618 INFO::Starting hierarchical adjustment
2024-07-22 01:13:22.026417 INFO::Found 5 batches.
2024-07-22 01:13:22.027711 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:22.029252 INFO::Using default BPPARAM
2024-07-22 01:13:22.030588 INFO::Processing subtree level 1
2024-07-22 01:13:22.282211 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:22.294935 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:22.352604 INFO::Done
2024-07-22 01:13:22.354113 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:22.366032 INFO::ASW Batch was 0.135920191887013 prior to batch effect correction and is now -0.0747912484637752 .
2024-07-22 01:13:22.367698 INFO::ASW Label was 0.567691681686271 prior to batch effect correction and is now 0.839290607470238 .
2024-07-22 01:13:22.369945 INFO::Total function execution time is 0.381302833557129 s and adjustment time is 0.326529026031494 s ( 85.64 )
2024-07-22 01:13:22.415386 INFO::Formatting Data.
2024-07-22 01:13:22.417207 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:22.419532 INFO::Removing potential empty rows and columns
2024-07-22 01:13:22.422942 INFO::Found 0 missing values.
2024-07-22 01:13:22.43062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:22.432138 INFO::Done
2024-07-22 01:13:22.433381 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:22.440401 INFO::Starting hierarchical adjustment
2024-07-22 01:13:22.444173 INFO::Found 2 batches.
2024-07-22 01:13:22.445666 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:22.447192 INFO::Using default BPPARAM
2024-07-22 01:13:22.448374 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:22.450494 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:22.499879 INFO::Done
2024-07-22 01:13:22.5015 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:22.510211 INFO::ASW Batch was 0.524166752973588 prior to batch effect correction and is now 0.0602286836629094 .
2024-07-22 01:13:22.511719 INFO::ASW Label was 0.536653611121454 prior to batch effect correction and is now 0.87437294174623 .
2024-07-22 01:13:22.513614 INFO::Total function execution time is 0.0983591079711914 s and adjustment time is 0.0560169219970703 s ( 56.95 )
2024-07-22 01:13:22.516916 INFO::Formatting Data.
2024-07-22 01:13:22.518542 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:22.520722 INFO::Removing potential empty rows and columns
2024-07-22 01:13:22.523194 INFO::Found 0 missing values.
2024-07-22 01:13:22.531113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:22.532546 INFO::Done
2024-07-22 01:13:22.533805 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:22.54167 INFO::Starting hierarchical adjustment
2024-07-22 01:13:22.544243 INFO::Found 2 batches.
2024-07-22 01:13:22.546788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:22.548477 INFO::Using default BPPARAM
2024-07-22 01:13:22.54983 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:22.55205 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:22.599665 INFO::Done
2024-07-22 01:13:22.601188 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:22.611934 INFO::ASW Batch was 0.524166752973588 prior to batch effect correction and is now 0.0602286836629094 .
2024-07-22 01:13:22.613479 INFO::ASW Label was 0.536653611121454 prior to batch effect correction and is now 0.87437294174623 .
2024-07-22 01:13:22.615397 INFO::Total function execution time is 0.0986258983612061 s and adjustment time is 0.0560100078582764 s ( 56.79 )
2024-07-22 01:13:22.653057 INFO::Formatting Data.
2024-07-22 01:13:22.654802 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:22.660277 INFO::Removing potential empty rows and columns
2024-07-22 01:13:22.662721 INFO::Found 0 missing values.
2024-07-22 01:13:22.668383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:22.670906 INFO::Done
2024-07-22 01:13:22.67231 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:22.676842 INFO::Starting hierarchical adjustment
2024-07-22 01:13:22.678658 INFO::Found 2 batches.
2024-07-22 01:13:22.683133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:22.685066 INFO::Using default BPPARAM
2024-07-22 01:13:22.686341 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:22.688409 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:22.796149 INFO::Done
2024-07-22 01:13:22.797681 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:22.802131 INFO::ASW Batch was -0.124725986774284 prior to batch effect correction and is now -0.125038476622177 .
2024-07-22 01:13:22.804086 INFO::Total function execution time is 0.15115213394165 s and adjustment time is 0.11634087562561 s ( 76.97 )
2024-07-22 01:13:22.84299 INFO::Formatting Data.
2024-07-22 01:13:22.844825 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:22.846768 INFO::Removing potential empty rows and columns
2024-07-22 01:13:22.849245 INFO::Found 0 missing values.
2024-07-22 01:13:22.852094 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.
2024-07-22 01:13:22.872822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:22.874319 INFO::Done
2024-07-22 01:13:22.875561 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:22.884992 INFO::Starting hierarchical adjustment
2024-07-22 01:13:22.886991 INFO::Found 2 batches.
2024-07-22 01:13:22.88831 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:22.88975 INFO::Using default BPPARAM
2024-07-22 01:13:22.890961 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:22.895774 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:22.950003 INFO::Done
2024-07-22 01:13:22.951447 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:22.960264 INFO::ASW Batch was 0.435644376546207 prior to batch effect correction and is now -0.0361360830149474 .
2024-07-22 01:13:22.961719 INFO::ASW Label was 0.633448617918503 prior to batch effect correction and is now 0.944642263569481 .
2024-07-22 01:13:22.963366 INFO::Total function execution time is 0.121379852294922 s and adjustment time is 0.063406229019165 s ( 52.24 )
2024-07-22 01:13:22.965275 INFO::Formatting Data.
2024-07-22 01:13:22.968137 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:22.97055 INFO::Removing potential empty rows and columns
2024-07-22 01:13:22.973069 INFO::Found 0 missing values.
2024-07-22 01:13:22.975641 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.
2024-07-22 01:13:22.992372 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:22.994024 INFO::Done
2024-07-22 01:13:22.9957 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:23.006208 INFO::Starting hierarchical adjustment
2024-07-22 01:13:23.008439 INFO::Found 2 batches.
2024-07-22 01:13:23.009745 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:23.011306 INFO::Using default BPPARAM
2024-07-22 01:13:23.012858 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:23.015087 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:23.069564 INFO::Done
2024-07-22 01:13:23.070958 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:23.078993 INFO::ASW Batch was 0.435644376546207 prior to batch effect correction and is now -0.0361360830149474 .
2024-07-22 01:13:23.0804 INFO::ASW Label was 0.633448617918503 prior to batch effect correction and is now 0.944642263569481 .
2024-07-22 01:13:23.082581 INFO::Total function execution time is 0.117357969284058 s and adjustment time is 0.061668872833252 s ( 52.55 )
2024-07-22 01:13:23.799133 INFO::Formatting Data.
2024-07-22 01:13:23.800781 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:23.805621 INFO::Removing potential empty rows and columns
2024-07-22 01:13:23.808575 INFO::Found 0 missing values.
2024-07-22 01:13:23.820052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:23.821886 INFO::Done
2024-07-22 01:13:23.823166 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:23.83305 INFO::Starting hierarchical adjustment
2024-07-22 01:13:23.834835 INFO::Found 3 batches.
2024-07-22 01:13:23.835994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:23.837702 INFO::Using default BPPARAM
2024-07-22 01:13:23.838972 INFO::Processing subtree level 1
2024-07-22 01:13:24.08735 INFO::Adjusting the last 1 batches sequentially
2024-07-22 01:13:24.095043 INFO::Done
2024-07-22 01:13:24.097173 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:24.113055 INFO::ASW Batch was -0.0134493500491961 prior to batch effect correction and is now -0.0134493500491961 .
2024-07-22 01:13:24.11689 INFO::Total function execution time is 0.317808151245117 s and adjustment time is 0.260499000549316 s ( 81.97 )
2024-07-22 01:13:24.119097 INFO::Formatting Data.
2024-07-22 01:13:24.12114 INFO::Typecasting input to dataframe.
2024-07-22 01:13:24.123517 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:24.127023 INFO::Removing potential empty rows and columns
2024-07-22 01:13:24.130415 INFO::Found 0 missing values.
2024-07-22 01:13:24.140404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:24.142123 INFO::Done
2024-07-22 01:13:24.144897 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:24.151106 INFO::Starting hierarchical adjustment
2024-07-22 01:13:24.153033 INFO::Found 3 batches.
2024-07-22 01:13:24.154439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:24.155932 INFO::Using default BPPARAM
2024-07-22 01:13:24.157304 INFO::Processing subtree level 1
2024-07-22 01:13:24.396692 INFO::Adjusting the last 1 batches sequentially
2024-07-22 01:13:24.407794 INFO::Done
2024-07-22 01:13:24.411041 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:24.424604 INFO::ASW Batch was -0.0134493500491961 prior to batch effect correction and is now -0.0134493500491961 .
2024-07-22 01:13:24.427947 INFO::Total function execution time is 0.308762073516846 s and adjustment time is 0.2551109790802 s ( 82.62 )
2024-07-22 01:13:24.467087 INFO::Formatting Data.
2024-07-22 01:13:24.468763 INFO::Typecasting input to dataframe.
2024-07-22 01:13:24.4707 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:24.473304 INFO::Removing potential empty rows and columns
2024-07-22 01:13:24.476479 INFO::Found 0 missing values.
2024-07-22 01:13:24.489628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:24.491082 INFO::Done
2024-07-22 01:13:24.495826 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:24.504153 INFO::Starting hierarchical adjustment
2024-07-22 01:13:24.506102 INFO::Found 3 batches.
2024-07-22 01:13:24.508402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:24.510025 INFO::Using default BPPARAM
2024-07-22 01:13:24.511384 INFO::Processing subtree level 1
2024-07-22 01:13:24.749689 INFO::Adjusting the last 1 batches sequentially
2024-07-22 01:13:24.758741 INFO::Done
2024-07-22 01:13:24.762126 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:24.777034 INFO::ASW Batch was -0.04885871287406 prior to batch effect correction and is now -0.04885871287406 .
2024-07-22 01:13:24.78164 INFO::Total function execution time is 0.314560174942017 s and adjustment time is 0.253096103668213 s ( 80.46 )
2024-07-22 01:13:25.188245 INFO::Formatting Data.
2024-07-22 01:13:25.189869 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:25.192479 INFO::Removing potential empty rows and columns
2024-07-22 01:13:25.202269 INFO::Found 1000 missing values.
2024-07-22 01:13:25.279888 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:25.281366 INFO::Done
2024-07-22 01:13:25.282646 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:25.295286 INFO::Starting hierarchical adjustment
2024-07-22 01:13:25.297281 INFO::Found 10 batches.
2024-07-22 01:13:25.298676 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:25.300268 INFO::Using default BPPARAM
2024-07-22 01:13:25.302196 INFO::Processing subtree level 1
2024-07-22 01:13:25.644957 INFO::Processing subtree level 2
2024-07-22 01:13:26.094111 INFO::Adjusting the last 1 batches sequentially
2024-07-22 01:13:26.107633 INFO::Done
2024-07-22 01:13:26.110857 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:26.132893 INFO::ASW Batch was 0.478530426903881 prior to batch effect correction and is now 0.478530426903881 .
2024-07-22 01:13:26.134408 INFO::ASW Label was 0.35729376526231 prior to batch effect correction and is now 0.35729376526231 .
2024-07-22 01:13:26.141479 INFO::Total function execution time is 0.952502965927124 s and adjustment time is 0.810739994049072 s ( 85.12 )
2024-07-22 01:13:26.143937 INFO::Formatting Data.
2024-07-22 01:13:26.146572 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:26.150337 INFO::Removing potential empty rows and columns
2024-07-22 01:13:26.158912 INFO::Found 1000 missing values.
2024-07-22 01:13:26.217455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:26.218753 INFO::Done
2024-07-22 01:13:26.220114 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:26.232539 INFO::Starting hierarchical adjustment
2024-07-22 01:13:26.234369 INFO::Found 10 batches.
2024-07-22 01:13:27.845732 INFO::Set up parallel execution backend with 2 workers
2024-07-22 01:13:27.847027 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-22 01:13:29.99675 INFO::Adjusting the last 2 batches sequentially
2024-07-22 01:13:29.998799 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-22 01:13:30.051844 INFO::Done
2024-07-22 01:13:30.052986 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:30.065549 INFO::ASW Batch was 0.478530426903881 prior to batch effect correction and is now 0.478530426903881 .
2024-07-22 01:13:30.066718 INFO::ASW Label was 0.35729376526231 prior to batch effect correction and is now 0.35729376526231 .
2024-07-22 01:13:30.06878 INFO::Total function execution time is 3.92438101768494 s and adjustment time is 3.81788682937622 s ( 97.29 )
2024-07-22 01:13:30.508754 INFO::Formatting Data.
2024-07-22 01:13:30.510547 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:30.512755 INFO::Removing potential empty rows and columns
2024-07-22 01:13:30.516584 INFO::Found 0 missing values.
2024-07-22 01:13:30.529639 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:30.531928 INFO::Done
2024-07-22 01:13:30.534624 INFO::Acquiring quality metrics before batch effect correction.
2024-07-22 01:13:30.541176 INFO::Starting hierarchical adjustment
2024-07-22 01:13:30.543077 INFO::Found 3 batches.
2024-07-22 01:13:30.544488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-22 01:13:30.546081 INFO::Using default BPPARAM
2024-07-22 01:13:30.547434 INFO::Processing subtree level 1
2024-07-22 01:13:30.857328 INFO::Adjusting the last 1 batches sequentially
2024-07-22 01:13:30.866587 INFO::Done
2024-07-22 01:13:30.869819 INFO::Acquiring quality metrics after batch effect correction.
2024-07-22 01:13:30.887525 INFO::ASW Batch was 0.230151316132586 prior to batch effect correction and is now -0.143205205080605 .
2024-07-22 01:13:30.890433 INFO::ASW Label was -0.217957221642949 prior to batch effect correction and is now -0.191913444040982 .
2024-07-22 01:13:30.894415 INFO::Total function execution time is 0.385517120361328 s and adjustment time is 0.323869943618774 s ( 84.01 )
2024-07-22 01:13:31.28366 INFO::Formatting Data.
2024-07-22 01:13:31.285491 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:31.287954 INFO::Removing potential empty rows and columns
2024-07-22 01:13:31.291072 INFO::Found 2 missing values.
2024-07-22 01:13:31.301644 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:31.303161 INFO::Done
2024-07-22 01:13:31.405494 INFO::Found NA in Reference column
2024-07-22 01:13:31.43956 INFO::Require at least two references per batch.
2024-07-22 01:13:31.512052 INFO::Formatting Data.
2024-07-22 01:13:31.513671 INFO::Recognized SummarizedExperiment
2024-07-22 01:13:31.515003 INFO::Typecasting input to dataframe.
2024-07-22 01:13:31.549224 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:31.551927 INFO::Removing potential empty rows and columns
2024-07-22 01:13:31.565912 INFO::Found 0 missing values.
2024-07-22 01:13:31.59128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:31.592588 INFO::Done
2024-07-22 01:13:31.648598 INFO::Formatting Data.
2024-07-22 01:13:31.650283 INFO::Recognized SummarizedExperiment
2024-07-22 01:13:31.651666 INFO::Typecasting input to dataframe.
2024-07-22 01:13:31.711322 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:31.714124 INFO::Removing potential empty rows and columns
2024-07-22 01:13:31.726979 INFO::Found 0 missing values.
2024-07-22 01:13:31.778615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:31.780249 INFO::Done
2024-07-22 01:13:31.844619 INFO::Formatting Data.
2024-07-22 01:13:31.850602 INFO::Recognized SummarizedExperiment
2024-07-22 01:13:31.852142 INFO::Typecasting input to dataframe.
2024-07-22 01:13:31.919986 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:31.92668 INFO::Removing potential empty rows and columns
2024-07-22 01:13:31.930039 INFO::Found 0 missing values.
2024-07-22 01:13:31.933209 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.
2024-07-22 01:13:31.952526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:31.953989 INFO::Done
2024-07-22 01:13:31.989954 INFO::Formatting Data.
2024-07-22 01:13:31.991806 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:31.994237 INFO::Removing potential empty rows and columns
2024-07-22 01:13:31.997178 INFO::Found 0 missing values.
2024-07-22 01:13:32.006414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:32.00824 INFO::Done
2024-07-22 01:13:32.05627 INFO::Formatting Data.
2024-07-22 01:13:32.058127 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:32.06035 INFO::Removing potential empty rows and columns
2024-07-22 01:13:32.06372 INFO::Found 0 missing values.
2024-07-22 01:13:32.075534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:32.077138 INFO::Done
2024-07-22 01:13:32.186239 INFO::Formatting Data.
2024-07-22 01:13:32.188086 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:32.191312 INFO::Removing potential empty rows and columns
2024-07-22 01:13:32.194683 INFO::Found 1 missing values.
2024-07-22 01:13:32.203818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:32.205711 INFO::Done
2024-07-22 01:13:32.277031 INFO::Formatting Data.
2024-07-22 01:13:32.278669 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:32.280928 INFO::Removing potential empty rows and columns
2024-07-22 01:13:32.284468 INFO::Found 2 missing values.
2024-07-22 01:13:32.287417 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.
2024-07-22 01:13:32.29372 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:32.298782 INFO::Done
2024-07-22 01:13:32.334946 INFO::Formatting Data.
2024-07-22 01:13:32.340236 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:32.342886 INFO::Removing potential empty rows and columns
2024-07-22 01:13:32.345545 INFO::Found 2 missing values.
2024-07-22 01:13:32.350428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:32.355495 INFO::Done
2024-07-22 01:13:32.393281 INFO::Formatting Data.
2024-07-22 01:13:32.395042 INFO::Typecasting input to dataframe.
2024-07-22 01:13:32.396926 INFO::Replacing NaNs with NAs.
2024-07-22 01:13:32.398842 INFO::Removing potential empty rows and columns
2024-07-22 01:13:32.402431 INFO::Found 0 missing values.
2024-07-22 01:13:32.411364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-22 01:13:32.413768 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.544 6.195 49.709
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 45.588 | 2.770 | 40.957 | |
| compute_asw | 0.058 | 0.002 | 0.073 | |
| count_existing | 0.027 | 0.001 | 0.032 | |
| generate_data_covariables | 0.026 | 0.002 | 0.032 | |
| generate_dataset | 0.025 | 0.003 | 0.029 | |