Yannis Schumann
| Snapshot Date: 2024-07-04 14:00 -0400 (Thu, 04 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-05 11:38 -0400 (Fri, 05 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" | 4593 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4399 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3688 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 154/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-07-04 20:41:15 -0400 (Thu, 04 Jul 2024) |
| EndedAt: 2024-07-04 20:42:42 -0400 (Thu, 04 Jul 2024) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 24.429 1.074 17.42
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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-pc-linux-gnu
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")
2024-07-04 20:42:06.971543 INFO::Formatting Data.
2024-07-04 20:42:06.973402 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:06.989369 INFO::Removing potential empty rows and columns
2024-07-04 20:42:07.333567 INFO::Found 0 missing values.
2024-07-04 20:42:07.337334 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:07.338081 INFO::Done
2024-07-04 20:42:07.338705 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:07.352574 INFO::Starting hierarchical adjustment
2024-07-04 20:42:07.353458 INFO::Found 3 batches.
2024-07-04 20:42:07.354075 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:07.355384 INFO::Using default BPPARAM
2024-07-04 20:42:07.355961 INFO::Processing subtree level 1
2024-07-04 20:42:07.449341 INFO::Adjusting the last 1 batches sequentially
2024-07-04 20:42:07.451365 INFO::Done
2024-07-04 20:42:07.452059 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:07.454943 INFO::ASW Batch was -0.105545423964534 prior to batch effect correction and is now -0.105545423964534 .
2024-07-04 20:42:07.4561 INFO::Total function execution time is 0.485668420791626 s and adjustment time is 0.097869873046875 s ( 20.15 )
2024-07-04 20:42:07.472815 INFO::Formatting Data.
2024-07-04 20:42:07.473572 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:07.474605 INFO::Removing potential empty rows and columns
2024-07-04 20:42:07.475915 INFO::Found 0 missing values.
2024-07-04 20:42:07.476972 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.
2024-07-04 20:42:07.489998 INFO::Formatting Data.
2024-07-04 20:42:07.490755 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:07.491766 INFO::Removing potential empty rows and columns
2024-07-04 20:42:07.49295 INFO::Found 0 missing values.
2024-07-04 20:42:07.494055 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.
2024-07-04 20:42:07.510391 INFO::Formatting Data.
2024-07-04 20:42:07.511095 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:07.51194 INFO::Removing potential empty rows and columns
2024-07-04 20:42:07.512902 INFO::Found 0 missing values.
2024-07-04 20:42:07.513762 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.
2024-07-04 20:42:07.517924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:07.518436 INFO::Done
2024-07-04 20:42:07.518908 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:07.520905 INFO::Starting hierarchical adjustment
2024-07-04 20:42:07.521546 INFO::Found 2 batches.
2024-07-04 20:42:07.522049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:07.522614 INFO::Using default BPPARAM
2024-07-04 20:42:07.523114 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:07.52401 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:07.546127 INFO::Done
2024-07-04 20:42:07.546786 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:07.548755 INFO::ASW Batch was 0.0763951683149161 prior to batch effect correction and is now -0.131675216225682 .
2024-07-04 20:42:07.549488 INFO::Total function execution time is 0.0391581058502197 s and adjustment time is 0.0246930122375488 s ( 63.06 )
2024-07-04 20:42:07.552317 INFO::Formatting Data.
2024-07-04 20:42:07.552907 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:07.561236 INFO::Formatting Data.
2024-07-04 20:42:07.561842 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:07.562643 INFO::Removing potential empty rows and columns
2024-07-04 20:42:07.563609 INFO::Found 0 missing values.
2024-07-04 20:42:07.569956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:07.570602 INFO::Done
2024-07-04 20:42:07.571105 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:07.573353 INFO::Starting hierarchical adjustment
2024-07-04 20:42:07.574026 INFO::Found 2 batches.
2024-07-04 20:42:07.574515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:07.575099 INFO::Using default BPPARAM
2024-07-04 20:42:07.575595 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:07.576491 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:07.592461 INFO::Done
2024-07-04 20:42:07.593095 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:07.595097 INFO::ASW Batch was 0.0142511787009296 prior to batch effect correction and is now -0.1136279531821 .
2024-07-04 20:42:07.595924 INFO::Total function execution time is 0.0346767902374268 s and adjustment time is 0.0185666084289551 s ( 53.54 )
2024-07-04 20:42:07.597038 INFO::Formatting Data.
2024-07-04 20:42:07.597606 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:07.598498 INFO::Removing potential empty rows and columns
2024-07-04 20:42:07.5996 INFO::Found 0 missing values.
2024-07-04 20:42:07.602458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:07.602977 INFO::Done
2024-07-04 20:42:07.603459 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:07.605373 INFO::Starting hierarchical adjustment
2024-07-04 20:42:07.606047 INFO::Found 2 batches.
2024-07-04 20:42:07.606525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:07.607072 INFO::Using default BPPARAM
2024-07-04 20:42:07.607545 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:07.608389 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:07.623078 INFO::Done
2024-07-04 20:42:07.62368 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:07.625623 INFO::ASW Batch was 0.0142511787009296 prior to batch effect correction and is now -0.1136279531821 .
2024-07-04 20:42:07.626359 INFO::Total function execution time is 0.0293252468109131 s and adjustment time is 0.0171699523925781 s ( 58.55 )
2024-07-04 20:42:09.771257 INFO::Formatting Data.
2024-07-04 20:42:09.771998 INFO::Recognized SummarizedExperiment
2024-07-04 20:42:09.772472 INFO::Typecasting input to dataframe.
2024-07-04 20:42:09.827992 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:09.829082 INFO::Removing potential empty rows and columns
2024-07-04 20:42:09.832024 INFO::Found 0 missing values.
2024-07-04 20:42:09.837502 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:09.837979 INFO::Done
2024-07-04 20:42:09.83841 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:09.841362 INFO::Starting hierarchical adjustment
2024-07-04 20:42:09.841941 INFO::Found 2 batches.
2024-07-04 20:42:09.842365 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:09.843295 INFO::Using default BPPARAM
2024-07-04 20:42:09.843723 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:09.844559 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:09.889908 INFO::Done
2024-07-04 20:42:09.89049 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:09.893344 INFO::ASW Batch was 0.010753110540313 prior to batch effect correction and is now -0.0903274523422092 .
2024-07-04 20:42:09.894064 INFO::Total function execution time is 0.123143434524536 s and adjustment time is 0.0480611324310303 s ( 39.03 )
2024-07-04 20:42:09.908947 INFO::Formatting Data.
2024-07-04 20:42:09.909547 INFO::Recognized SummarizedExperiment
2024-07-04 20:42:09.909979 INFO::Typecasting input to dataframe.
2024-07-04 20:42:09.917374 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:09.918305 INFO::Removing potential empty rows and columns
2024-07-04 20:42:09.921063 INFO::Found 0 missing values.
2024-07-04 20:42:09.926348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:09.926802 INFO::Done
2024-07-04 20:42:09.927231 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:09.933867 INFO::Starting hierarchical adjustment
2024-07-04 20:42:09.934571 INFO::Found 2 batches.
2024-07-04 20:42:09.935029 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:09.935552 INFO::Using default BPPARAM
2024-07-04 20:42:09.936006 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:09.936885 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:09.958019 INFO::Done
2024-07-04 20:42:09.95864 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:09.961684 INFO::ASW Batch was 0.0106381560540836 prior to batch effect correction and is now 0.0106381560540836 .
2024-07-04 20:42:09.962457 INFO::Total function execution time is 0.0534915924072266 s and adjustment time is 0.0235767364501953 s ( 44.08 )
2024-07-04 20:42:09.97852 INFO::Formatting Data.
2024-07-04 20:42:09.979178 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:09.979973 INFO::Removing potential empty rows and columns
2024-07-04 20:42:09.980872 INFO::Found 0 missing values.
2024-07-04 20:42:09.983312 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:09.983764 INFO::Done
2024-07-04 20:42:09.984188 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:09.985883 INFO::Starting hierarchical adjustment
2024-07-04 20:42:09.986456 INFO::Found 3 batches.
2024-07-04 20:42:09.986886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:09.987376 INFO::Using default BPPARAM
2024-07-04 20:42:09.987803 INFO::Processing subtree level 1
2024-07-04 20:42:10.125825 INFO::Adjusting the last 1 batches sequentially
2024-07-04 20:42:10.127489 INFO::Done
2024-07-04 20:42:10.128076 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:10.130414 INFO::ASW Batch was -0.0912880226333515 prior to batch effect correction and is now -0.167607986974495 .
2024-07-04 20:42:10.131325 INFO::Total function execution time is 0.152793645858765 s and adjustment time is 0.141124248504639 s ( 92.36 )
2024-07-04 20:42:10.145914 INFO::Skipping initial DF formatting
2024-07-04 20:42:10.146584 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:10.150676 INFO::Starting hierarchical adjustment
2024-07-04 20:42:10.151402 INFO::Found 5 batches.
2024-07-04 20:42:10.151909 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:10.152533 INFO::Using default BPPARAM
2024-07-04 20:42:10.153052 INFO::Processing subtree level 1
2024-07-04 20:42:10.279009 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:10.280628 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:10.300352 INFO::Done
2024-07-04 20:42:10.301029 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:10.305026 INFO::ASW Batch was 0.56661984793004 prior to batch effect correction and is now 0.56661984793004 .
2024-07-04 20:42:10.305592 INFO::ASW Label was 0.373835970084971 prior to batch effect correction and is now 0.373835970084971 .
2024-07-04 20:42:10.306364 INFO::Total function execution time is 0.160524368286133 s and adjustment time is 0.149084806442261 s ( 92.87 )
2024-07-04 20:42:10.322493 INFO::Formatting Data.
2024-07-04 20:42:10.32326 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:10.324188 INFO::Removing potential empty rows and columns
2024-07-04 20:42:10.32522 INFO::Found 0 missing values.
2024-07-04 20:42:10.329271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:10.329786 INFO::Done
2024-07-04 20:42:10.33029 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:10.333367 INFO::Starting hierarchical adjustment
2024-07-04 20:42:10.334091 INFO::Found 5 batches.
2024-07-04 20:42:10.334608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:10.335202 INFO::Using default BPPARAM
2024-07-04 20:42:10.335706 INFO::Processing subtree level 1
2024-07-04 20:42:10.482983 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:10.484691 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:10.502296 INFO::Done
2024-07-04 20:42:10.503112 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:10.506408 INFO::ASW Batch was 0.560874879523499 prior to batch effect correction and is now -0.0658796131642623 .
2024-07-04 20:42:10.507043 INFO::ASW Label was 0.250496773529127 prior to batch effect correction and is now 0.727323360482261 .
2024-07-04 20:42:10.507861 INFO::Total function execution time is 0.185434818267822 s and adjustment time is 0.16829776763916 s ( 90.76 )
2024-07-04 20:42:10.508746 INFO::Formatting Data.
2024-07-04 20:42:10.509372 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:10.510225 INFO::Removing potential empty rows and columns
2024-07-04 20:42:10.511178 INFO::Found 0 missing values.
2024-07-04 20:42:10.515192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:10.515728 INFO::Done
2024-07-04 20:42:10.516249 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:10.519234 INFO::Starting hierarchical adjustment
2024-07-04 20:42:10.519937 INFO::Found 5 batches.
2024-07-04 20:42:10.520472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:10.521093 INFO::Using default BPPARAM
2024-07-04 20:42:10.521653 INFO::Processing subtree level 1
2024-07-04 20:42:10.634129 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:10.635746 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:10.651447 INFO::Done
2024-07-04 20:42:10.65219 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:10.655466 INFO::ASW Batch was 0.560874879523499 prior to batch effect correction and is now -0.0658796131642623 .
2024-07-04 20:42:10.656075 INFO::ASW Label was 0.250496773529127 prior to batch effect correction and is now 0.727323360482261 .
2024-07-04 20:42:10.656889 INFO::Total function execution time is 0.148135900497437 s and adjustment time is 0.131624937057495 s ( 88.85 )
2024-07-04 20:42:10.670063 INFO::Formatting Data.
2024-07-04 20:42:10.670846 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:10.671756 INFO::Removing potential empty rows and columns
2024-07-04 20:42:10.672777 INFO::Found 0 missing values.
2024-07-04 20:42:10.676763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:10.677292 INFO::Done
2024-07-04 20:42:10.677794 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:10.680846 INFO::Starting hierarchical adjustment
2024-07-04 20:42:10.681535 INFO::Found 5 batches.
2024-07-04 20:42:10.68207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:10.682685 INFO::Using default BPPARAM
2024-07-04 20:42:10.683192 INFO::Processing subtree level 1
2024-07-04 20:42:10.817822 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:10.819764 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:10.835665 INFO::Done
2024-07-04 20:42:10.836422 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:10.839705 INFO::ASW Batch was 0.305357060685674 prior to batch effect correction and is now -0.0407274401480689 .
2024-07-04 20:42:10.840322 INFO::ASW Label was 0.410983769109092 prior to batch effect correction and is now 0.749376314621654 .
2024-07-04 20:42:10.841192 INFO::Total function execution time is 0.171195268630981 s and adjustment time is 0.154227495193481 s ( 90.09 )
2024-07-04 20:42:10.842055 INFO::Formatting Data.
2024-07-04 20:42:10.843323 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:10.844443 INFO::Removing potential empty rows and columns
2024-07-04 20:42:10.845506 INFO::Found 0 missing values.
2024-07-04 20:42:10.849512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:10.850076 INFO::Done
2024-07-04 20:42:10.850581 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:10.853824 INFO::Starting hierarchical adjustment
2024-07-04 20:42:10.854557 INFO::Found 5 batches.
2024-07-04 20:42:10.85508 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:10.855671 INFO::Using default BPPARAM
2024-07-04 20:42:10.856169 INFO::Processing subtree level 1
2024-07-04 20:42:10.968231 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:10.969866 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:10.986468 INFO::Done
2024-07-04 20:42:10.987238 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:10.990396 INFO::ASW Batch was 0.305357060685674 prior to batch effect correction and is now -0.0407274401480689 .
2024-07-04 20:42:10.990983 INFO::ASW Label was 0.410983769109092 prior to batch effect correction and is now 0.749376314621654 .
2024-07-04 20:42:10.991754 INFO::Total function execution time is 0.149701833724976 s and adjustment time is 0.132023096084595 s ( 88.19 )
2024-07-04 20:42:11.004199 INFO::Formatting Data.
2024-07-04 20:42:11.004933 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.005807 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.006754 INFO::Found 0 missing values.
2024-07-04 20:42:11.009408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.009938 INFO::Done
2024-07-04 20:42:11.01046 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.01337 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.014065 INFO::Found 2 batches.
2024-07-04 20:42:11.014569 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.015182 INFO::Using default BPPARAM
2024-07-04 20:42:11.015679 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:11.016559 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:11.031184 INFO::Done
2024-07-04 20:42:11.031841 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.034805 INFO::ASW Batch was 0.695166023531939 prior to batch effect correction and is now -0.0310894897374166 .
2024-07-04 20:42:11.035379 INFO::ASW Label was 0.273517010301642 prior to batch effect correction and is now 0.867095231495787 .
2024-07-04 20:42:11.036166 INFO::Total function execution time is 0.0320339202880859 s and adjustment time is 0.0172467231750488 s ( 53.84 )
2024-07-04 20:42:11.036982 INFO::Formatting Data.
2024-07-04 20:42:11.03759 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.038441 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.039377 INFO::Found 0 missing values.
2024-07-04 20:42:11.042091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.042622 INFO::Done
2024-07-04 20:42:11.043115 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.045974 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.046644 INFO::Found 2 batches.
2024-07-04 20:42:11.047145 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.047709 INFO::Using default BPPARAM
2024-07-04 20:42:11.048198 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:11.049093 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:11.063296 INFO::Done
2024-07-04 20:42:11.063924 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.066795 INFO::ASW Batch was 0.695166023531939 prior to batch effect correction and is now -0.0310894897374166 .
2024-07-04 20:42:11.067331 INFO::ASW Label was 0.273517010301642 prior to batch effect correction and is now 0.867095231495787 .
2024-07-04 20:42:11.081924 INFO::Total function execution time is 0.0448970794677734 s and adjustment time is 0.0167884826660156 s ( 37.39 )
2024-07-04 20:42:11.092553 INFO::Formatting Data.
2024-07-04 20:42:11.093225 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.094048 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.094861 INFO::Found 0 missing values.
2024-07-04 20:42:11.096827 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.097352 INFO::Done
2024-07-04 20:42:11.097844 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.099627 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.100269 INFO::Found 2 batches.
2024-07-04 20:42:11.100753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.1013 INFO::Using default BPPARAM
2024-07-04 20:42:11.101766 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:11.102605 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:11.1327 INFO::Done
2024-07-04 20:42:11.133327 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.13521 INFO::ASW Batch was 0.315609094020872 prior to batch effect correction and is now -0.119595861062727 .
2024-07-04 20:42:11.135953 INFO::Total function execution time is 0.0434648990631104 s and adjustment time is 0.0325295925140381 s ( 74.84 )
2024-07-04 20:42:11.146898 INFO::Formatting Data.
2024-07-04 20:42:11.147591 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.148388 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.149349 INFO::Found 0 missing values.
2024-07-04 20:42:11.150502 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.
2024-07-04 20:42:11.155045 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.155579 INFO::Done
2024-07-04 20:42:11.156061 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.158975 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.159636 INFO::Found 2 batches.
2024-07-04 20:42:11.160131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.160693 INFO::Using default BPPARAM
2024-07-04 20:42:11.161172 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:11.162057 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:11.178572 INFO::Done
2024-07-04 20:42:11.17929 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.182119 INFO::ASW Batch was 0.436941291082677 prior to batch effect correction and is now 0.107993521171249 .
2024-07-04 20:42:11.182672 INFO::ASW Label was 0.679452999080096 prior to batch effect correction and is now 0.875210620300121 .
2024-07-04 20:42:11.183419 INFO::Total function execution time is 0.0365891456604004 s and adjustment time is 0.0190596580505371 s ( 52.09 )
2024-07-04 20:42:11.184148 INFO::Formatting Data.
2024-07-04 20:42:11.184762 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.185611 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.186531 INFO::Found 0 missing values.
2024-07-04 20:42:11.187367 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.
2024-07-04 20:42:11.191634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.192125 INFO::Done
2024-07-04 20:42:11.192642 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.195488 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.19612 INFO::Found 2 batches.
2024-07-04 20:42:11.196624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.19716 INFO::Using default BPPARAM
2024-07-04 20:42:11.197608 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:11.198454 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:11.214194 INFO::Done
2024-07-04 20:42:11.214815 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.217571 INFO::ASW Batch was 0.436941291082677 prior to batch effect correction and is now 0.107993521171249 .
2024-07-04 20:42:11.218101 INFO::ASW Label was 0.679452999080096 prior to batch effect correction and is now 0.875210620300121 .
2024-07-04 20:42:11.218815 INFO::Total function execution time is 0.0346748828887939 s and adjustment time is 0.0181910991668701 s ( 52.46 )
2024-07-04 20:42:11.41351 INFO::Formatting Data.
2024-07-04 20:42:11.414331 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.415251 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.416274 INFO::Found 0 missing values.
2024-07-04 20:42:11.41924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.419779 INFO::Done
2024-07-04 20:42:11.420277 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.422338 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.423044 INFO::Found 3 batches.
2024-07-04 20:42:11.423547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.424132 INFO::Using default BPPARAM
2024-07-04 20:42:11.424655 INFO::Processing subtree level 1
2024-07-04 20:42:11.51968 INFO::Adjusting the last 1 batches sequentially
2024-07-04 20:42:11.522495 INFO::Done
2024-07-04 20:42:11.523365 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.52656 INFO::ASW Batch was -0.0430066383738076 prior to batch effect correction and is now -0.0430066383738076 .
2024-07-04 20:42:11.527702 INFO::Total function execution time is 0.114194869995117 s and adjustment time is 0.0995383262634277 s ( 87.17 )
2024-07-04 20:42:11.528937 INFO::Formatting Data.
2024-07-04 20:42:11.529648 INFO::Typecasting input to dataframe.
2024-07-04 20:42:11.530504 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.53161 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.532957 INFO::Found 0 missing values.
2024-07-04 20:42:11.542995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.544353 INFO::Done
2024-07-04 20:42:11.545022 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.548463 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.54939 INFO::Found 3 batches.
2024-07-04 20:42:11.54996 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.550687 INFO::Using default BPPARAM
2024-07-04 20:42:11.551239 INFO::Processing subtree level 1
2024-07-04 20:42:11.647444 INFO::Adjusting the last 1 batches sequentially
2024-07-04 20:42:11.649133 INFO::Done
2024-07-04 20:42:11.649758 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.652064 INFO::ASW Batch was -0.0430066383738076 prior to batch effect correction and is now -0.0430066383738076 .
2024-07-04 20:42:11.653081 INFO::Total function execution time is 0.124143838882446 s and adjustment time is 0.0999584197998047 s ( 80.52 )
2024-07-04 20:42:11.666228 INFO::Formatting Data.
2024-07-04 20:42:11.66696 INFO::Typecasting input to dataframe.
2024-07-04 20:42:11.667742 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.668631 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.669684 INFO::Found 0 missing values.
2024-07-04 20:42:11.672514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.673032 INFO::Done
2024-07-04 20:42:11.673547 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.675457 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.676174 INFO::Found 3 batches.
2024-07-04 20:42:11.676714 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.677321 INFO::Using default BPPARAM
2024-07-04 20:42:11.677833 INFO::Processing subtree level 1
2024-07-04 20:42:11.770988 INFO::Adjusting the last 1 batches sequentially
2024-07-04 20:42:11.772871 INFO::Done
2024-07-04 20:42:11.773506 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:11.776008 INFO::ASW Batch was -0.0202198765169064 prior to batch effect correction and is now -0.0202198765169064 .
2024-07-04 20:42:11.777005 INFO::Total function execution time is 0.110786437988281 s and adjustment time is 0.0968055725097656 s ( 87.38 )
2024-07-04 20:42:11.929477 INFO::Formatting Data.
2024-07-04 20:42:11.930257 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:11.931409 INFO::Removing potential empty rows and columns
2024-07-04 20:42:11.934109 INFO::Found 1000 missing values.
2024-07-04 20:42:11.953057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:11.953814 INFO::Done
2024-07-04 20:42:11.954373 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:11.960057 INFO::Starting hierarchical adjustment
2024-07-04 20:42:11.960869 INFO::Found 10 batches.
2024-07-04 20:42:11.961432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:11.962076 INFO::Using default BPPARAM
2024-07-04 20:42:11.962638 INFO::Processing subtree level 1
2024-07-04 20:42:12.304795 INFO::Processing subtree level 2
2024-07-04 20:42:12.508579 INFO::Adjusting the last 1 batches sequentially
2024-07-04 20:42:12.510566 INFO::Done
2024-07-04 20:42:12.511201 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:12.516994 INFO::ASW Batch was 0.516879120350323 prior to batch effect correction and is now 0.516879120350323 .
2024-07-04 20:42:12.517626 INFO::ASW Label was 0.304346067914614 prior to batch effect correction and is now 0.304346067914614 .
2024-07-04 20:42:12.518548 INFO::Total function execution time is 0.58910870552063 s and adjustment time is 0.549832820892334 s ( 93.33 )
2024-07-04 20:42:12.519406 INFO::Formatting Data.
2024-07-04 20:42:12.520083 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:12.521552 INFO::Removing potential empty rows and columns
2024-07-04 20:42:12.524996 INFO::Found 1000 missing values.
2024-07-04 20:42:12.545269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:12.546084 INFO::Done
2024-07-04 20:42:12.546662 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:12.552899 INFO::Starting hierarchical adjustment
2024-07-04 20:42:12.55376 INFO::Found 10 batches.
2024-07-04 20:42:13.69135 INFO::Set up parallel execution backend with 2 workers
2024-07-04 20:42:13.692553 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-04 20:42:14.881392 INFO::Adjusting the last 2 batches sequentially
2024-07-04 20:42:14.882909 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-04 20:42:14.897992 INFO::Done
2024-07-04 20:42:14.898573 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:14.903004 INFO::ASW Batch was 0.516879120350323 prior to batch effect correction and is now 0.516879120350323 .
2024-07-04 20:42:14.903502 INFO::ASW Label was 0.304346067914614 prior to batch effect correction and is now 0.304346067914614 .
2024-07-04 20:42:14.904152 INFO::Total function execution time is 2.38481736183167 s and adjustment time is 2.34440851211548 s ( 98.31 )
2024-07-04 20:42:15.035933 INFO::Formatting Data.
2024-07-04 20:42:15.036747 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.03765 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.038784 INFO::Found 0 missing values.
2024-07-04 20:42:15.042359 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.042881 INFO::Done
2024-07-04 20:42:15.043382 INFO::Acquiring quality metrics before batch effect correction.
2024-07-04 20:42:15.046079 INFO::Starting hierarchical adjustment
2024-07-04 20:42:15.046765 INFO::Found 3 batches.
2024-07-04 20:42:15.047276 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-04 20:42:15.04785 INFO::Using default BPPARAM
2024-07-04 20:42:15.048346 INFO::Processing subtree level 1
2024-07-04 20:42:15.157873 INFO::Adjusting the last 1 batches sequentially
2024-07-04 20:42:15.15993 INFO::Done
2024-07-04 20:42:15.160672 INFO::Acquiring quality metrics after batch effect correction.
2024-07-04 20:42:15.164204 INFO::ASW Batch was 0.184157459426706 prior to batch effect correction and is now -0.172965443173324 .
2024-07-04 20:42:15.164858 INFO::ASW Label was -0.154793736541396 prior to batch effect correction and is now 0.0184690735234981 .
2024-07-04 20:42:15.165839 INFO::Total function execution time is 0.129903793334961 s and adjustment time is 0.113260746002197 s ( 87.19 )
2024-07-04 20:42:15.276186 INFO::Formatting Data.
2024-07-04 20:42:15.277037 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.277853 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.278816 INFO::Found 2 missing values.
2024-07-04 20:42:15.281418 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.281901 INFO::Done
2024-07-04 20:42:15.304744 INFO::Found NA in Reference column
2024-07-04 20:42:15.312956 INFO::Require at least two references per batch.
2024-07-04 20:42:15.331116 INFO::Formatting Data.
2024-07-04 20:42:15.331777 INFO::Recognized SummarizedExperiment
2024-07-04 20:42:15.332258 INFO::Typecasting input to dataframe.
2024-07-04 20:42:15.340944 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.341942 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.345124 INFO::Found 0 missing values.
2024-07-04 20:42:15.351054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.351533 INFO::Done
2024-07-04 20:42:15.364994 INFO::Formatting Data.
2024-07-04 20:42:15.365578 INFO::Recognized SummarizedExperiment
2024-07-04 20:42:15.366033 INFO::Typecasting input to dataframe.
2024-07-04 20:42:15.381606 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.382667 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.385806 INFO::Found 0 missing values.
2024-07-04 20:42:15.395527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.396068 INFO::Done
2024-07-04 20:42:15.410055 INFO::Formatting Data.
2024-07-04 20:42:15.41069 INFO::Recognized SummarizedExperiment
2024-07-04 20:42:15.411157 INFO::Typecasting input to dataframe.
2024-07-04 20:42:15.426103 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.426975 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.42793 INFO::Found 0 missing values.
2024-07-04 20:42:15.428776 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.
2024-07-04 20:42:15.43292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.433402 INFO::Done
2024-07-04 20:42:15.442643 INFO::Formatting Data.
2024-07-04 20:42:15.44334 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.444119 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.445035 INFO::Found 0 missing values.
2024-07-04 20:42:15.447763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.448275 INFO::Done
2024-07-04 20:42:15.457996 INFO::Formatting Data.
2024-07-04 20:42:15.458624 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.459456 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.460409 INFO::Found 0 missing values.
2024-07-04 20:42:15.463066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.463527 INFO::Done
2024-07-04 20:42:15.48857 INFO::Formatting Data.
2024-07-04 20:42:15.489301 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.49071 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.491719 INFO::Found 1 missing values.
2024-07-04 20:42:15.493989 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.494465 INFO::Done
2024-07-04 20:42:15.510823 INFO::Formatting Data.
2024-07-04 20:42:15.511535 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.512329 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.513196 INFO::Found 2 missing values.
2024-07-04 20:42:15.514011 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.
2024-07-04 20:42:15.51605 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.516544 INFO::Done
2024-07-04 20:42:15.525389 INFO::Formatting Data.
2024-07-04 20:42:15.526069 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.526867 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.527711 INFO::Found 2 missing values.
2024-07-04 20:42:15.529193 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.529667 INFO::Done
2024-07-04 20:42:15.539041 INFO::Formatting Data.
2024-07-04 20:42:15.53975 INFO::Typecasting input to dataframe.
2024-07-04 20:42:15.540475 INFO::Replacing NaNs with NAs.
2024-07-04 20:42:15.541239 INFO::Removing potential empty rows and columns
2024-07-04 20:42:15.542124 INFO::Found 0 missing values.
2024-07-04 20:42:15.544924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-04 20:42:15.545411 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.954 4.125 20.520
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.429 | 1.074 | 17.420 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.014 | 0.000 | 0.013 | |
| generate_data_covariables | 0.012 | 0.000 | 0.012 | |
| generate_dataset | 0.012 | 0.000 | 0.012 | |