Yannis Schumann
| Snapshot Date: 2024-07-25 14:00 -0400 (Thu, 25 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-26 11:40 -0400 (Fri, 26 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4690 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4384 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4406 |
| 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 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 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: 1.1.2 |
| 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_1.1.2.tar.gz |
| StartedAt: 2024-07-25 19:45:18 -0400 (Thu, 25 Jul 2024) |
| EndedAt: 2024-07-25 19:46:48 -0400 (Thu, 25 Jul 2024) |
| EllapsedTime: 90.1 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 28.96 1.688 20.878
* 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")
2024-07-25 19:46:26.194834 INFO::Formatting Data.
2024-07-25 19:46:26.199166 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:26.212825 INFO::Removing potential empty rows and columns
2024-07-25 19:46:26.550656 INFO::Found 0 missing values.
2024-07-25 19:46:26.555958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:26.557139 INFO::Done
2024-07-25 19:46:26.557775 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:26.57667 INFO::Starting hierarchical adjustment
2024-07-25 19:46:26.577666 INFO::Found 3 batches.
2024-07-25 19:46:26.578516 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:26.579803 INFO::Using default BPPARAM
2024-07-25 19:46:26.580313 INFO::Processing subtree level 1
2024-07-25 19:46:26.748747 INFO::Adjusting the last 1 batches sequentially
2024-07-25 19:46:26.754003 INFO::Done
2024-07-25 19:46:26.757134 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:26.762901 INFO::ASW Batch was -0.0378385878275746 prior to batch effect correction and is now -0.0378385878275746 .
2024-07-25 19:46:26.764786 INFO::Total function execution time is 0.571049928665161 s and adjustment time is 0.175684928894043 s ( 30.77 )
2024-07-25 19:46:26.788968 INFO::Formatting Data.
2024-07-25 19:46:26.78994 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:26.791447 INFO::Removing potential empty rows and columns
2024-07-25 19:46:26.793135 INFO::Found 0 missing values.
2024-07-25 19:46:26.79408 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.
2024-07-25 19:46:26.805901 INFO::Formatting Data.
2024-07-25 19:46:26.806754 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:26.808298 INFO::Removing potential empty rows and columns
2024-07-25 19:46:26.80933 INFO::Found 0 missing values.
2024-07-25 19:46:26.810277 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.
2024-07-25 19:46:26.831206 INFO::Formatting Data.
2024-07-25 19:46:26.832432 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:26.83384 INFO::Removing potential empty rows and columns
2024-07-25 19:46:26.835249 INFO::Found 0 missing values.
2024-07-25 19:46:26.836487 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.
2024-07-25 19:46:26.843565 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:26.844591 INFO::Done
2024-07-25 19:46:26.845688 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:26.848875 INFO::Starting hierarchical adjustment
2024-07-25 19:46:26.849949 INFO::Found 2 batches.
2024-07-25 19:46:26.850688 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:26.851539 INFO::Using default BPPARAM
2024-07-25 19:46:26.852249 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:26.853481 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:26.881374 INFO::Done
2024-07-25 19:46:26.882063 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:26.884112 INFO::ASW Batch was -0.0567092255603598 prior to batch effect correction and is now -0.126174528110026 .
2024-07-25 19:46:26.885151 INFO::Total function execution time is 0.0540201663970947 s and adjustment time is 0.0316429138183594 s ( 58.58 )
2024-07-25 19:46:26.888766 INFO::Formatting Data.
2024-07-25 19:46:26.88999 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:26.901329 INFO::Formatting Data.
2024-07-25 19:46:26.902469 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:26.90344 INFO::Removing potential empty rows and columns
2024-07-25 19:46:26.90477 INFO::Found 0 missing values.
2024-07-25 19:46:26.908981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:26.909916 INFO::Done
2024-07-25 19:46:26.910967 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:26.914426 INFO::Starting hierarchical adjustment
2024-07-25 19:46:26.915589 INFO::Found 2 batches.
2024-07-25 19:46:26.916455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:26.917333 INFO::Using default BPPARAM
2024-07-25 19:46:26.918117 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:26.919024 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:26.937631 INFO::Done
2024-07-25 19:46:26.938719 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:26.941806 INFO::ASW Batch was 0.0059792035946325 prior to batch effect correction and is now -0.121901632268527 .
2024-07-25 19:46:26.943052 INFO::Total function execution time is 0.0418579578399658 s and adjustment time is 0.0222549438476562 s ( 53.17 )
2024-07-25 19:46:26.944781 INFO::Formatting Data.
2024-07-25 19:46:26.945701 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:26.947042 INFO::Removing potential empty rows and columns
2024-07-25 19:46:26.94893 INFO::Found 0 missing values.
2024-07-25 19:46:26.95252 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:26.953343 INFO::Done
2024-07-25 19:46:26.954204 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:26.957267 INFO::Starting hierarchical adjustment
2024-07-25 19:46:26.958179 INFO::Found 2 batches.
2024-07-25 19:46:26.958737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:26.959263 INFO::Using default BPPARAM
2024-07-25 19:46:26.95972 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:26.960635 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:26.98081 INFO::Done
2024-07-25 19:46:26.981884 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:26.984802 INFO::ASW Batch was 0.0059792035946325 prior to batch effect correction and is now -0.121901632268527 .
2024-07-25 19:46:26.985957 INFO::Total function execution time is 0.0412108898162842 s and adjustment time is 0.0227479934692383 s ( 55.2 )
2024-07-25 19:46:29.785972 INFO::Formatting Data.
2024-07-25 19:46:29.786717 INFO::Recognized SummarizedExperiment
2024-07-25 19:46:29.787198 INFO::Typecasting input to dataframe.
2024-07-25 19:46:30.704812 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:30.706075 INFO::Removing potential empty rows and columns
2024-07-25 19:46:30.7089 INFO::Found 0 missing values.
2024-07-25 19:46:30.714428 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:30.71499 INFO::Done
2024-07-25 19:46:30.71542 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:30.718159 INFO::Starting hierarchical adjustment
2024-07-25 19:46:30.718757 INFO::Found 2 batches.
2024-07-25 19:46:30.719182 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:30.720457 INFO::Using default BPPARAM
2024-07-25 19:46:30.721061 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:30.722312 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:30.78154 INFO::Done
2024-07-25 19:46:30.782134 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:30.785724 INFO::ASW Batch was 0.00331000835040684 prior to batch effect correction and is now -0.0972499513038128 .
2024-07-25 19:46:30.786584 INFO::Total function execution time is 1.00093579292297 s and adjustment time is 0.0628747940063477 s ( 6.28 )
2024-07-25 19:46:30.809536 INFO::Formatting Data.
2024-07-25 19:46:30.81053 INFO::Recognized SummarizedExperiment
2024-07-25 19:46:30.811418 INFO::Typecasting input to dataframe.
2024-07-25 19:46:30.820779 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:30.822193 INFO::Removing potential empty rows and columns
2024-07-25 19:46:30.825553 INFO::Found 0 missing values.
2024-07-25 19:46:30.830972 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:30.831804 INFO::Done
2024-07-25 19:46:30.83253 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:30.835925 INFO::Starting hierarchical adjustment
2024-07-25 19:46:30.836792 INFO::Found 2 batches.
2024-07-25 19:46:30.837232 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:30.837712 INFO::Using default BPPARAM
2024-07-25 19:46:30.838331 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:30.839698 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:30.864215 INFO::Done
2024-07-25 19:46:30.864824 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:30.868373 INFO::ASW Batch was 0.00375148157316225 prior to batch effect correction and is now 0.00375148157316225 .
2024-07-25 19:46:30.869478 INFO::Total function execution time is 0.0599780082702637 s and adjustment time is 0.0275449752807617 s ( 45.93 )
2024-07-25 19:46:30.894135 INFO::Formatting Data.
2024-07-25 19:46:30.895488 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:30.896612 INFO::Removing potential empty rows and columns
2024-07-25 19:46:30.897792 INFO::Found 0 missing values.
2024-07-25 19:46:30.901134 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:30.901796 INFO::Done
2024-07-25 19:46:30.902512 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:30.905085 INFO::Starting hierarchical adjustment
2024-07-25 19:46:30.905914 INFO::Found 3 batches.
2024-07-25 19:46:30.906529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:30.907227 INFO::Using default BPPARAM
2024-07-25 19:46:30.907834 INFO::Processing subtree level 1
2024-07-25 19:46:31.139084 INFO::Adjusting the last 1 batches sequentially
2024-07-25 19:46:31.147362 INFO::Done
2024-07-25 19:46:31.150259 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:31.15969 INFO::ASW Batch was -0.0710311427270687 prior to batch effect correction and is now -0.170740958368715 .
2024-07-25 19:46:31.164693 INFO::Total function execution time is 0.269984006881714 s and adjustment time is 0.241477012634277 s ( 89.44 )
2024-07-25 19:46:31.191263 INFO::Skipping initial DF formatting
2024-07-25 19:46:31.192364 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:31.199959 INFO::Starting hierarchical adjustment
2024-07-25 19:46:31.201657 INFO::Found 5 batches.
2024-07-25 19:46:31.202362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:31.203139 INFO::Using default BPPARAM
2024-07-25 19:46:31.203706 INFO::Processing subtree level 1
2024-07-25 19:46:31.416669 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:31.435823 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:31.480249 INFO::Done
2024-07-25 19:46:31.480959 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:31.487581 INFO::ASW Batch was 0.49826221788475 prior to batch effect correction and is now 0.49826221788475 .
2024-07-25 19:46:31.488369 INFO::ASW Label was 0.410123531722805 prior to batch effect correction and is now 0.410123531722805 .
2024-07-25 19:46:31.489325 INFO::Total function execution time is 0.298243045806885 s and adjustment time is 0.279249906539917 s ( 93.63 )
2024-07-25 19:46:31.516462 INFO::Formatting Data.
2024-07-25 19:46:31.517251 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:31.518151 INFO::Removing potential empty rows and columns
2024-07-25 19:46:31.519077 INFO::Found 0 missing values.
2024-07-25 19:46:31.522744 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:31.523268 INFO::Done
2024-07-25 19:46:31.523748 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:31.527872 INFO::Starting hierarchical adjustment
2024-07-25 19:46:31.528624 INFO::Found 5 batches.
2024-07-25 19:46:31.529111 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:31.52967 INFO::Using default BPPARAM
2024-07-25 19:46:31.530152 INFO::Processing subtree level 1
2024-07-25 19:46:31.686385 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:31.700993 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:31.742219 INFO::Done
2024-07-25 19:46:31.74353 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:31.748472 INFO::ASW Batch was 0.361700419873559 prior to batch effect correction and is now -0.0594397644475081 .
2024-07-25 19:46:31.752442 INFO::ASW Label was 0.36609484697879 prior to batch effect correction and is now 0.846590373762313 .
2024-07-25 19:46:31.754112 INFO::Total function execution time is 0.237594127655029 s and adjustment time is 0.213697195053101 s ( 89.94 )
2024-07-25 19:46:31.758443 INFO::Formatting Data.
2024-07-25 19:46:31.759489 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:31.761377 INFO::Removing potential empty rows and columns
2024-07-25 19:46:31.763004 INFO::Found 0 missing values.
2024-07-25 19:46:31.768934 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:31.769905 INFO::Done
2024-07-25 19:46:31.770897 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:31.774739 INFO::Starting hierarchical adjustment
2024-07-25 19:46:31.775501 INFO::Found 5 batches.
2024-07-25 19:46:31.776049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:31.776612 INFO::Using default BPPARAM
2024-07-25 19:46:31.777075 INFO::Processing subtree level 1
2024-07-25 19:46:31.939903 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:31.953535 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:31.988428 INFO::Done
2024-07-25 19:46:31.989716 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:31.99893 INFO::ASW Batch was 0.361700419873559 prior to batch effect correction and is now -0.0594397644475081 .
2024-07-25 19:46:32.000008 INFO::ASW Label was 0.36609484697879 prior to batch effect correction and is now 0.846590373762313 .
2024-07-25 19:46:32.002773 INFO::Total function execution time is 0.244323968887329 s and adjustment time is 0.212992906570435 s ( 87.18 )
2024-07-25 19:46:32.029935 INFO::Formatting Data.
2024-07-25 19:46:32.030908 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:32.032641 INFO::Removing potential empty rows and columns
2024-07-25 19:46:32.034552 INFO::Found 0 missing values.
2024-07-25 19:46:32.040267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:32.041153 INFO::Done
2024-07-25 19:46:32.042082 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:32.04565 INFO::Starting hierarchical adjustment
2024-07-25 19:46:32.04664 INFO::Found 5 batches.
2024-07-25 19:46:32.047156 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:32.048102 INFO::Using default BPPARAM
2024-07-25 19:46:32.048837 INFO::Processing subtree level 1
2024-07-25 19:46:32.207954 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:32.222898 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:32.260466 INFO::Done
2024-07-25 19:46:32.26139 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:32.266256 INFO::ASW Batch was 0.360507341695979 prior to batch effect correction and is now -0.0199670083688875 .
2024-07-25 19:46:32.267181 INFO::ASW Label was 0.39071849375983 prior to batch effect correction and is now 0.816714595596806 .
2024-07-25 19:46:32.268924 INFO::Total function execution time is 0.238929033279419 s and adjustment time is 0.213937044143677 s ( 89.54 )
2024-07-25 19:46:32.270954 INFO::Formatting Data.
2024-07-25 19:46:32.271617 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:32.273928 INFO::Removing potential empty rows and columns
2024-07-25 19:46:32.274922 INFO::Found 0 missing values.
2024-07-25 19:46:32.281269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:32.2819 INFO::Done
2024-07-25 19:46:32.282707 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:32.28751 INFO::Starting hierarchical adjustment
2024-07-25 19:46:32.288682 INFO::Found 5 batches.
2024-07-25 19:46:32.289494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:32.290392 INFO::Using default BPPARAM
2024-07-25 19:46:32.290928 INFO::Processing subtree level 1
2024-07-25 19:46:32.442236 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:32.462247 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:32.511505 INFO::Done
2024-07-25 19:46:32.512979 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:32.518628 INFO::ASW Batch was 0.360507341695979 prior to batch effect correction and is now -0.0199670083688875 .
2024-07-25 19:46:32.519545 INFO::ASW Label was 0.39071849375983 prior to batch effect correction and is now 0.816714595596806 .
2024-07-25 19:46:32.520729 INFO::Total function execution time is 0.24987006187439 s and adjustment time is 0.223006010055542 s ( 89.25 )
2024-07-25 19:46:32.542491 INFO::Formatting Data.
2024-07-25 19:46:32.543624 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:32.544721 INFO::Removing potential empty rows and columns
2024-07-25 19:46:32.546777 INFO::Found 0 missing values.
2024-07-25 19:46:32.550486 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:32.551222 INFO::Done
2024-07-25 19:46:32.551951 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:32.555646 INFO::Starting hierarchical adjustment
2024-07-25 19:46:32.556567 INFO::Found 2 batches.
2024-07-25 19:46:32.557379 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:32.558709 INFO::Using default BPPARAM
2024-07-25 19:46:32.559449 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:32.560937 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:32.581044 INFO::Done
2024-07-25 19:46:32.582087 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:32.586329 INFO::ASW Batch was 0.452450080475584 prior to batch effect correction and is now -0.0215398993730976 .
2024-07-25 19:46:32.587226 INFO::ASW Label was 0.590672562782036 prior to batch effect correction and is now 0.951608398116584 .
2024-07-25 19:46:32.588486 INFO::Total function execution time is 0.0461080074310303 s and adjustment time is 0.0245440006256104 s ( 53.23 )
2024-07-25 19:46:32.589385 INFO::Formatting Data.
2024-07-25 19:46:32.590161 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:32.591672 INFO::Removing potential empty rows and columns
2024-07-25 19:46:32.593033 INFO::Found 0 missing values.
2024-07-25 19:46:32.596926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:32.597759 INFO::Done
2024-07-25 19:46:32.598426 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:32.602016 INFO::Starting hierarchical adjustment
2024-07-25 19:46:32.603088 INFO::Found 2 batches.
2024-07-25 19:46:32.603801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:32.604587 INFO::Using default BPPARAM
2024-07-25 19:46:32.605357 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:32.606628 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:32.625742 INFO::Done
2024-07-25 19:46:32.626678 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:32.631707 INFO::ASW Batch was 0.452450080475584 prior to batch effect correction and is now -0.0215398993730976 .
2024-07-25 19:46:32.632816 INFO::ASW Label was 0.590672562782036 prior to batch effect correction and is now 0.951608398116584 .
2024-07-25 19:46:32.63374 INFO::Total function execution time is 0.0443680286407471 s and adjustment time is 0.0228350162506104 s ( 51.47 )
2024-07-25 19:46:32.649273 INFO::Formatting Data.
2024-07-25 19:46:32.650031 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:32.65086 INFO::Removing potential empty rows and columns
2024-07-25 19:46:32.651704 INFO::Found 0 missing values.
2024-07-25 19:46:32.653798 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:32.654467 INFO::Done
2024-07-25 19:46:32.655237 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:32.658016 INFO::Starting hierarchical adjustment
2024-07-25 19:46:32.658715 INFO::Found 2 batches.
2024-07-25 19:46:32.659197 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:32.659717 INFO::Using default BPPARAM
2024-07-25 19:46:32.66017 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:32.66102 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:32.695925 INFO::Done
2024-07-25 19:46:32.696808 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:32.69881 INFO::ASW Batch was -0.105457537238476 prior to batch effect correction and is now -0.152135647924382 .
2024-07-25 19:46:32.700331 INFO::Total function execution time is 0.0510551929473877 s and adjustment time is 0.0373141765594482 s ( 73.09 )
2024-07-25 19:46:32.719738 INFO::Formatting Data.
2024-07-25 19:46:32.72049 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:32.721748 INFO::Removing potential empty rows and columns
2024-07-25 19:46:32.722939 INFO::Found 0 missing values.
2024-07-25 19:46:32.724083 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.
2024-07-25 19:46:32.729339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:32.730159 INFO::Done
2024-07-25 19:46:32.730903 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:32.734645 INFO::Starting hierarchical adjustment
2024-07-25 19:46:32.735349 INFO::Found 2 batches.
2024-07-25 19:46:32.735827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:32.736349 INFO::Using default BPPARAM
2024-07-25 19:46:32.736797 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:32.738087 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:32.758958 INFO::Done
2024-07-25 19:46:32.759959 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:32.763348 INFO::ASW Batch was 0.736195110258419 prior to batch effect correction and is now 0.0309059965788635 .
2024-07-25 19:46:32.764251 INFO::ASW Label was 0.321924336094415 prior to batch effect correction and is now 0.846584048256103 .
2024-07-25 19:46:32.765305 INFO::Total function execution time is 0.0456039905548096 s and adjustment time is 0.0236580371856689 s ( 51.88 )
2024-07-25 19:46:32.766387 INFO::Formatting Data.
2024-07-25 19:46:32.7672 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:32.768423 INFO::Removing potential empty rows and columns
2024-07-25 19:46:32.769757 INFO::Found 0 missing values.
2024-07-25 19:46:32.770996 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.
2024-07-25 19:46:32.777457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:32.778319 INFO::Done
2024-07-25 19:46:32.779057 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:32.783216 INFO::Starting hierarchical adjustment
2024-07-25 19:46:32.783991 INFO::Found 2 batches.
2024-07-25 19:46:32.78451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:32.785047 INFO::Using default BPPARAM
2024-07-25 19:46:32.785721 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:32.786978 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:32.807117 INFO::Done
2024-07-25 19:46:32.807874 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:32.81185 INFO::ASW Batch was 0.736195110258419 prior to batch effect correction and is now 0.0309059965788635 .
2024-07-25 19:46:32.812824 INFO::ASW Label was 0.321924336094415 prior to batch effect correction and is now 0.846584048256103 .
2024-07-25 19:46:32.813971 INFO::Total function execution time is 0.047637939453125 s and adjustment time is 0.0232439041137695 s ( 48.79 )
2024-07-25 19:46:33.102206 INFO::Formatting Data.
2024-07-25 19:46:33.103305 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:33.104486 INFO::Removing potential empty rows and columns
2024-07-25 19:46:33.10585 INFO::Found 0 missing values.
2024-07-25 19:46:33.110023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:33.110872 INFO::Done
2024-07-25 19:46:33.111538 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:33.11406 INFO::Starting hierarchical adjustment
2024-07-25 19:46:33.115003 INFO::Found 3 batches.
2024-07-25 19:46:33.116021 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:33.116928 INFO::Using default BPPARAM
2024-07-25 19:46:33.11741 INFO::Processing subtree level 1
2024-07-25 19:46:33.27985 INFO::Adjusting the last 1 batches sequentially
2024-07-25 19:46:33.302117 INFO::Done
2024-07-25 19:46:33.307406 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:33.319423 INFO::ASW Batch was -0.125274072245262 prior to batch effect correction and is now -0.125274072245262 .
2024-07-25 19:46:33.322117 INFO::Total function execution time is 0.219978094100952 s and adjustment time is 0.18718409538269 s ( 85.09 )
2024-07-25 19:46:33.32432 INFO::Formatting Data.
2024-07-25 19:46:33.325877 INFO::Typecasting input to dataframe.
2024-07-25 19:46:33.327029 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:33.32939 INFO::Removing potential empty rows and columns
2024-07-25 19:46:33.332675 INFO::Found 0 missing values.
2024-07-25 19:46:33.338655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:33.340516 INFO::Done
2024-07-25 19:46:33.341834 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:33.345339 INFO::Starting hierarchical adjustment
2024-07-25 19:46:33.347115 INFO::Found 3 batches.
2024-07-25 19:46:33.347919 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:33.3488 INFO::Using default BPPARAM
2024-07-25 19:46:33.350078 INFO::Processing subtree level 1
2024-07-25 19:46:33.509105 INFO::Adjusting the last 1 batches sequentially
2024-07-25 19:46:33.519717 INFO::Done
2024-07-25 19:46:33.523305 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:33.53773 INFO::ASW Batch was -0.125274072245262 prior to batch effect correction and is now -0.125274072245262 .
2024-07-25 19:46:33.540859 INFO::Total function execution time is 0.216516971588135 s and adjustment time is 0.172808170318604 s ( 79.81 )
2024-07-25 19:46:33.568566 INFO::Formatting Data.
2024-07-25 19:46:33.569538 INFO::Typecasting input to dataframe.
2024-07-25 19:46:33.570555 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:33.572224 INFO::Removing potential empty rows and columns
2024-07-25 19:46:33.575241 INFO::Found 0 missing values.
2024-07-25 19:46:33.579313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:33.58019 INFO::Done
2024-07-25 19:46:33.580831 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:33.583612 INFO::Starting hierarchical adjustment
2024-07-25 19:46:33.584779 INFO::Found 3 batches.
2024-07-25 19:46:33.587263 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:33.588377 INFO::Using default BPPARAM
2024-07-25 19:46:33.589219 INFO::Processing subtree level 1
2024-07-25 19:46:33.729864 INFO::Adjusting the last 1 batches sequentially
2024-07-25 19:46:33.733082 INFO::Done
2024-07-25 19:46:33.734026 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:33.738149 INFO::ASW Batch was -0.120828391546087 prior to batch effect correction and is now -0.120828391546087 .
2024-07-25 19:46:33.739744 INFO::Total function execution time is 0.17120099067688 s and adjustment time is 0.148504018783569 s ( 86.74 )
2024-07-25 19:46:33.946866 INFO::Formatting Data.
2024-07-25 19:46:33.948244 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:33.949937 INFO::Removing potential empty rows and columns
2024-07-25 19:46:33.952717 INFO::Found 1000 missing values.
2024-07-25 19:46:33.974526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:33.975269 INFO::Done
2024-07-25 19:46:33.975811 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:33.982226 INFO::Starting hierarchical adjustment
2024-07-25 19:46:33.983113 INFO::Found 10 batches.
2024-07-25 19:46:33.983927 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:33.984819 INFO::Using default BPPARAM
2024-07-25 19:46:33.985596 INFO::Processing subtree level 1
2024-07-25 19:46:34.143185 INFO::Processing subtree level 2
2024-07-25 19:46:34.336229 INFO::Adjusting the last 1 batches sequentially
2024-07-25 19:46:34.341884 INFO::Done
2024-07-25 19:46:34.342737 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:34.351756 INFO::ASW Batch was 0.504583290818377 prior to batch effect correction and is now 0.504583290818377 .
2024-07-25 19:46:34.352855 INFO::ASW Label was 0.315561431017856 prior to batch effect correction and is now 0.315561431017856 .
2024-07-25 19:46:34.354736 INFO::Total function execution time is 0.40775990486145 s and adjustment time is 0.358962774276733 s ( 88.03 )
2024-07-25 19:46:34.356606 INFO::Formatting Data.
2024-07-25 19:46:34.357334 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:34.358653 INFO::Removing potential empty rows and columns
2024-07-25 19:46:34.363205 INFO::Found 1000 missing values.
2024-07-25 19:46:34.391587 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:34.392439 INFO::Done
2024-07-25 19:46:34.393652 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:34.399842 INFO::Starting hierarchical adjustment
2024-07-25 19:46:34.401279 INFO::Found 10 batches.
2024-07-25 19:46:35.860531 INFO::Set up parallel execution backend with 2 workers
2024-07-25 19:46:35.861447 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-25 19:46:37.260135 INFO::Adjusting the last 2 batches sequentially
2024-07-25 19:46:37.262023 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 19:46:37.283516 INFO::Done
2024-07-25 19:46:37.284142 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:37.289468 INFO::ASW Batch was 0.504583290818377 prior to batch effect correction and is now 0.504583290818377 .
2024-07-25 19:46:37.290384 INFO::ASW Label was 0.315561431017856 prior to batch effect correction and is now 0.315561431017856 .
2024-07-25 19:46:37.291413 INFO::Total function execution time is 2.93486905097961 s and adjustment time is 2.88257312774658 s ( 98.22 )
2024-07-25 19:46:37.594992 INFO::Formatting Data.
2024-07-25 19:46:37.59672 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:37.598926 INFO::Removing potential empty rows and columns
2024-07-25 19:46:37.600574 INFO::Found 0 missing values.
2024-07-25 19:46:37.606846 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:37.607864 INFO::Done
2024-07-25 19:46:37.608827 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 19:46:37.61301 INFO::Starting hierarchical adjustment
2024-07-25 19:46:37.614749 INFO::Found 3 batches.
2024-07-25 19:46:37.615308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 19:46:37.61668 INFO::Using default BPPARAM
2024-07-25 19:46:37.617413 INFO::Processing subtree level 1
2024-07-25 19:46:37.794803 INFO::Adjusting the last 1 batches sequentially
2024-07-25 19:46:37.815081 INFO::Done
2024-07-25 19:46:37.829791 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 19:46:37.844781 INFO::ASW Batch was 0.258917225559255 prior to batch effect correction and is now -0.170970844858303 .
2024-07-25 19:46:37.846298 INFO::ASW Label was -0.141271554363526 prior to batch effect correction and is now 0.212728128464684 .
2024-07-25 19:46:37.851883 INFO::Total function execution time is 0.256860971450806 s and adjustment time is 0.200401067733765 s ( 78.02 )
2024-07-25 19:46:38.050105 INFO::Formatting Data.
2024-07-25 19:46:38.051201 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.052291 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.054406 INFO::Found 2 missing values.
2024-07-25 19:46:38.057876 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.058545 INFO::Done
2024-07-25 19:46:38.106408 INFO::Found NA in Reference column
2024-07-25 19:46:38.121483 INFO::Require at least two references per batch.
2024-07-25 19:46:38.153479 INFO::Formatting Data.
2024-07-25 19:46:38.154747 INFO::Recognized SummarizedExperiment
2024-07-25 19:46:38.155341 INFO::Typecasting input to dataframe.
2024-07-25 19:46:38.166078 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.1679 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.171337 INFO::Found 0 missing values.
2024-07-25 19:46:38.18205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.183093 INFO::Done
2024-07-25 19:46:38.206282 INFO::Formatting Data.
2024-07-25 19:46:38.207378 INFO::Recognized SummarizedExperiment
2024-07-25 19:46:38.208263 INFO::Typecasting input to dataframe.
2024-07-25 19:46:38.234821 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.2366 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.240525 INFO::Found 0 missing values.
2024-07-25 19:46:38.25409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.255124 INFO::Done
2024-07-25 19:46:38.278047 INFO::Formatting Data.
2024-07-25 19:46:38.279099 INFO::Recognized SummarizedExperiment
2024-07-25 19:46:38.279893 INFO::Typecasting input to dataframe.
2024-07-25 19:46:38.302433 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.303436 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.304599 INFO::Found 0 missing values.
2024-07-25 19:46:38.305451 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.
2024-07-25 19:46:38.311862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.3127 INFO::Done
2024-07-25 19:46:38.330003 INFO::Formatting Data.
2024-07-25 19:46:38.331179 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.332137 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.333193 INFO::Found 0 missing values.
2024-07-25 19:46:38.336714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.337425 INFO::Done
2024-07-25 19:46:38.355192 INFO::Formatting Data.
2024-07-25 19:46:38.356403 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.357754 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.35918 INFO::Found 0 missing values.
2024-07-25 19:46:38.362714 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.363613 INFO::Done
2024-07-25 19:46:38.412715 INFO::Formatting Data.
2024-07-25 19:46:38.413895 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.415397 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.417042 INFO::Found 1 missing values.
2024-07-25 19:46:38.420981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.42178 INFO::Done
2024-07-25 19:46:38.450959 INFO::Formatting Data.
2024-07-25 19:46:38.452125 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.453441 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.454844 INFO::Found 2 missing values.
2024-07-25 19:46:38.456196 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.
2024-07-25 19:46:38.459491 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.460273 INFO::Done
2024-07-25 19:46:38.477457 INFO::Formatting Data.
2024-07-25 19:46:38.478344 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.479432 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.480782 INFO::Found 2 missing values.
2024-07-25 19:46:38.48241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.482919 INFO::Done
2024-07-25 19:46:38.500511 INFO::Formatting Data.
2024-07-25 19:46:38.501501 INFO::Typecasting input to dataframe.
2024-07-25 19:46:38.502706 INFO::Replacing NaNs with NAs.
2024-07-25 19:46:38.504006 INFO::Removing potential empty rows and columns
2024-07-25 19:46:38.505638 INFO::Found 0 missing values.
2024-07-25 19:46:38.509172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 19:46:38.510041 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.632 4.436 26.699
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.960 | 1.688 | 20.878 | |
| compute_asw | 0.026 | 0.003 | 0.028 | |
| count_existing | 0.014 | 0.001 | 0.015 | |
| generate_data_covariables | 0.016 | 0.002 | 0.017 | |
| generate_dataset | 0.014 | 0.001 | 0.015 | |