Yannis Schumann
| Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-12 17:38 -0400 (Fri, 12 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-07-10 20:46:36 -0400 (Wed, 10 Jul 2024) |
| EndedAt: 2024-07-10 20:48:03 -0400 (Wed, 10 Jul 2024) |
| EllapsedTime: 87.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-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 ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 24.424 1.59 17.885
* 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-3.19-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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")
2024-07-10 20:47:28.352286 INFO::Formatting Data.
2024-07-10 20:47:28.353817 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:28.364491 INFO::Removing potential empty rows and columns
2024-07-10 20:47:28.616376 INFO::Found 0 missing values.
2024-07-10 20:47:28.619387 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:28.619965 INFO::Done
2024-07-10 20:47:28.620453 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:28.631414 INFO::Starting hierarchical adjustment
2024-07-10 20:47:28.632223 INFO::Found 3 batches.
2024-07-10 20:47:28.63272 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:28.633738 INFO::Using default BPPARAM
2024-07-10 20:47:28.634244 INFO::Processing subtree level 1
2024-07-10 20:47:28.719057 INFO::Adjusting the last 1 batches sequentially
2024-07-10 20:47:28.720683 INFO::Done
2024-07-10 20:47:28.72128 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:28.723633 INFO::ASW Batch was -0.10433467896342 prior to batch effect correction and is now -0.10433467896342 .
2024-07-10 20:47:28.724645 INFO::Total function execution time is 0.37325119972229 s and adjustment time is 0.0886082649230957 s ( 23.74 )
2024-07-10 20:47:28.737696 INFO::Formatting Data.
2024-07-10 20:47:28.738389 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:28.739266 INFO::Removing potential empty rows and columns
2024-07-10 20:47:28.740323 INFO::Found 0 missing values.
2024-07-10 20:47:28.741221 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.
2024-07-10 20:47:28.7517 INFO::Formatting Data.
2024-07-10 20:47:28.757447 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:28.758678 INFO::Removing potential empty rows and columns
2024-07-10 20:47:28.759835 INFO::Found 0 missing values.
2024-07-10 20:47:28.760917 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.
2024-07-10 20:47:28.778581 INFO::Formatting Data.
2024-07-10 20:47:28.779316 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:28.780159 INFO::Removing potential empty rows and columns
2024-07-10 20:47:28.781117 INFO::Found 0 missing values.
2024-07-10 20:47:28.781971 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.
2024-07-10 20:47:28.786081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:28.786579 INFO::Done
2024-07-10 20:47:28.787076 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:28.789302 INFO::Starting hierarchical adjustment
2024-07-10 20:47:28.789953 INFO::Found 2 batches.
2024-07-10 20:47:28.790465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:28.791118 INFO::Using default BPPARAM
2024-07-10 20:47:28.791618 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:28.792507 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:28.814536 INFO::Done
2024-07-10 20:47:28.815159 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:28.81703 INFO::ASW Batch was 0.035373297828687 prior to batch effect correction and is now -0.1242168960149 .
2024-07-10 20:47:28.817775 INFO::Total function execution time is 0.0392463207244873 s and adjustment time is 0.0247125625610352 s ( 62.97 )
2024-07-10 20:47:28.820317 INFO::Formatting Data.
2024-07-10 20:47:28.820892 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:28.828823 INFO::Formatting Data.
2024-07-10 20:47:28.829421 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:28.830216 INFO::Removing potential empty rows and columns
2024-07-10 20:47:28.831164 INFO::Found 0 missing values.
2024-07-10 20:47:28.833803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:28.834284 INFO::Done
2024-07-10 20:47:28.83476 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:28.836603 INFO::Starting hierarchical adjustment
2024-07-10 20:47:28.837247 INFO::Found 2 batches.
2024-07-10 20:47:28.837735 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:28.838305 INFO::Using default BPPARAM
2024-07-10 20:47:28.838796 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:28.839632 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:28.853355 INFO::Done
2024-07-10 20:47:28.853933 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:28.855766 INFO::ASW Batch was -0.00989723102880788 prior to batch effect correction and is now -0.111247053690513 .
2024-07-10 20:47:28.856506 INFO::Total function execution time is 0.0276861190795898 s and adjustment time is 0.0162374973297119 s ( 58.65 )
2024-07-10 20:47:28.857512 INFO::Formatting Data.
2024-07-10 20:47:28.85808 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:28.85887 INFO::Removing potential empty rows and columns
2024-07-10 20:47:28.859825 INFO::Found 0 missing values.
2024-07-10 20:47:28.862426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:28.862918 INFO::Done
2024-07-10 20:47:28.863402 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:28.865234 INFO::Starting hierarchical adjustment
2024-07-10 20:47:28.865888 INFO::Found 2 batches.
2024-07-10 20:47:28.866372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:28.866933 INFO::Using default BPPARAM
2024-07-10 20:47:28.867418 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:28.868252 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:28.881946 INFO::Done
2024-07-10 20:47:28.882511 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:28.88436 INFO::ASW Batch was -0.00989723102880788 prior to batch effect correction and is now -0.111247053690513 .
2024-07-10 20:47:28.885062 INFO::Total function execution time is 0.0275518894195557 s and adjustment time is 0.0162019729614258 s ( 58.81 )
2024-07-10 20:47:31.021666 INFO::Formatting Data.
2024-07-10 20:47:31.022419 INFO::Recognized SummarizedExperiment
2024-07-10 20:47:31.022946 INFO::Typecasting input to dataframe.
2024-07-10 20:47:31.05294 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:31.054115 INFO::Removing potential empty rows and columns
2024-07-10 20:47:31.057585 INFO::Found 0 missing values.
2024-07-10 20:47:31.064028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:31.064544 INFO::Done
2024-07-10 20:47:31.065008 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:31.068277 INFO::Starting hierarchical adjustment
2024-07-10 20:47:31.068922 INFO::Found 2 batches.
2024-07-10 20:47:31.069378 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:31.070351 INFO::Using default BPPARAM
2024-07-10 20:47:31.070837 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:31.071707 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:31.14811 INFO::Done
2024-07-10 20:47:31.148742 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:31.1515 INFO::ASW Batch was -0.00320608931895205 prior to batch effect correction and is now -0.0867153581177631 .
2024-07-10 20:47:31.152209 INFO::Total function execution time is 0.130887985229492 s and adjustment time is 0.0793213844299316 s ( 60.6 )
2024-07-10 20:47:31.166872 INFO::Formatting Data.
2024-07-10 20:47:31.167516 INFO::Recognized SummarizedExperiment
2024-07-10 20:47:31.167989 INFO::Typecasting input to dataframe.
2024-07-10 20:47:31.17545 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:31.176403 INFO::Removing potential empty rows and columns
2024-07-10 20:47:31.179249 INFO::Found 0 missing values.
2024-07-10 20:47:31.184631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:31.185092 INFO::Done
2024-07-10 20:47:31.185539 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:31.188336 INFO::Starting hierarchical adjustment
2024-07-10 20:47:31.188942 INFO::Found 2 batches.
2024-07-10 20:47:31.189377 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:31.189869 INFO::Using default BPPARAM
2024-07-10 20:47:31.190312 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:31.191131 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:31.210174 INFO::Done
2024-07-10 20:47:31.210721 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:31.21359 INFO::ASW Batch was 0.0234723318211046 prior to batch effect correction and is now 0.0234723318211046 .
2024-07-10 20:47:31.214278 INFO::Total function execution time is 0.0473928451538086 s and adjustment time is 0.0213499069213867 s ( 45.05 )
2024-07-10 20:47:31.229331 INFO::Formatting Data.
2024-07-10 20:47:31.22993 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:31.23068 INFO::Removing potential empty rows and columns
2024-07-10 20:47:31.231546 INFO::Found 0 missing values.
2024-07-10 20:47:31.233993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:31.234445 INFO::Done
2024-07-10 20:47:31.234898 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:31.236583 INFO::Starting hierarchical adjustment
2024-07-10 20:47:31.237168 INFO::Found 3 batches.
2024-07-10 20:47:31.237612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:31.238138 INFO::Using default BPPARAM
2024-07-10 20:47:31.238584 INFO::Processing subtree level 1
2024-07-10 20:47:31.401395 INFO::Adjusting the last 1 batches sequentially
2024-07-10 20:47:31.403471 INFO::Done
2024-07-10 20:47:31.404166 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:31.406937 INFO::ASW Batch was -0.0799069941725388 prior to batch effect correction and is now -0.182470402970097 .
2024-07-10 20:47:31.407956 INFO::Total function execution time is 0.178553342819214 s and adjustment time is 0.166389226913452 s ( 93.19 )
2024-07-10 20:47:31.426841 INFO::Skipping initial DF formatting
2024-07-10 20:47:31.427665 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:31.432859 INFO::Starting hierarchical adjustment
2024-07-10 20:47:31.433788 INFO::Found 5 batches.
2024-07-10 20:47:31.434425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:31.435238 INFO::Using default BPPARAM
2024-07-10 20:47:31.435866 INFO::Processing subtree level 1
2024-07-10 20:47:31.57621 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:31.5778 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:31.59744 INFO::Done
2024-07-10 20:47:31.598118 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:31.602207 INFO::ASW Batch was 0.522936698933234 prior to batch effect correction and is now 0.522936698933234 .
2024-07-10 20:47:31.602809 INFO::ASW Label was 0.367223441656938 prior to batch effect correction and is now 0.367223441656938 .
2024-07-10 20:47:31.603628 INFO::Total function execution time is 0.176886796951294 s and adjustment time is 0.163886547088623 s ( 92.65 )
2024-07-10 20:47:31.620008 INFO::Formatting Data.
2024-07-10 20:47:31.620739 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:31.621623 INFO::Removing potential empty rows and columns
2024-07-10 20:47:31.622612 INFO::Found 0 missing values.
2024-07-10 20:47:31.626403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:31.626901 INFO::Done
2024-07-10 20:47:31.627386 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:31.630348 INFO::Starting hierarchical adjustment
2024-07-10 20:47:31.631028 INFO::Found 5 batches.
2024-07-10 20:47:31.631526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:31.632116 INFO::Using default BPPARAM
2024-07-10 20:47:31.632658 INFO::Processing subtree level 1
2024-07-10 20:47:31.745181 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:31.746619 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:31.761119 INFO::Done
2024-07-10 20:47:31.761833 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:31.76498 INFO::ASW Batch was 0.24875092317704 prior to batch effect correction and is now 0.00977363673633721 .
2024-07-10 20:47:31.76558 INFO::ASW Label was 0.538301350063475 prior to batch effect correction and is now 0.788567343290688 .
2024-07-10 20:47:31.766398 INFO::Total function execution time is 0.146461486816406 s and adjustment time is 0.130215167999268 s ( 88.91 )
2024-07-10 20:47:31.767243 INFO::Formatting Data.
2024-07-10 20:47:31.767889 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:31.768757 INFO::Removing potential empty rows and columns
2024-07-10 20:47:31.769713 INFO::Found 0 missing values.
2024-07-10 20:47:31.773715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:31.774249 INFO::Done
2024-07-10 20:47:31.774769 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:31.777597 INFO::Starting hierarchical adjustment
2024-07-10 20:47:31.778296 INFO::Found 5 batches.
2024-07-10 20:47:31.778823 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:31.779438 INFO::Using default BPPARAM
2024-07-10 20:47:31.780018 INFO::Processing subtree level 1
2024-07-10 20:47:31.883882 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:31.885395 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:31.900138 INFO::Done
2024-07-10 20:47:31.900845 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:31.903873 INFO::ASW Batch was 0.24875092317704 prior to batch effect correction and is now 0.00977363673633721 .
2024-07-10 20:47:31.904461 INFO::ASW Label was 0.538301350063475 prior to batch effect correction and is now 0.788567343290688 .
2024-07-10 20:47:31.905237 INFO::Total function execution time is 0.137993574142456 s and adjustment time is 0.121947765350342 s ( 88.37 )
2024-07-10 20:47:31.917511 INFO::Formatting Data.
2024-07-10 20:47:31.918185 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:31.919029 INFO::Removing potential empty rows and columns
2024-07-10 20:47:31.919969 INFO::Found 0 missing values.
2024-07-10 20:47:31.924003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:31.924512 INFO::Done
2024-07-10 20:47:31.925016 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:31.927796 INFO::Starting hierarchical adjustment
2024-07-10 20:47:31.928486 INFO::Found 5 batches.
2024-07-10 20:47:31.928994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:31.929577 INFO::Using default BPPARAM
2024-07-10 20:47:31.930116 INFO::Processing subtree level 1
2024-07-10 20:47:32.036182 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:32.037796 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:32.053279 INFO::Done
2024-07-10 20:47:32.053975 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.05725 INFO::ASW Batch was 0.260885121335415 prior to batch effect correction and is now -0.075656145402863 .
2024-07-10 20:47:32.057845 INFO::ASW Label was 0.465010085400402 prior to batch effect correction and is now 0.794167436567838 .
2024-07-10 20:47:32.058633 INFO::Total function execution time is 0.141130685806274 s and adjustment time is 0.124920606613159 s ( 88.51 )
2024-07-10 20:47:32.059488 INFO::Formatting Data.
2024-07-10 20:47:32.060116 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.060986 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.062008 INFO::Found 0 missing values.
2024-07-10 20:47:32.065943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.066477 INFO::Done
2024-07-10 20:47:32.067001 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.069981 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.070646 INFO::Found 5 batches.
2024-07-10 20:47:32.071159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.071758 INFO::Using default BPPARAM
2024-07-10 20:47:32.072301 INFO::Processing subtree level 1
2024-07-10 20:47:32.173646 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:32.175079 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:32.189401 INFO::Done
2024-07-10 20:47:32.190066 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.193098 INFO::ASW Batch was 0.260885121335415 prior to batch effect correction and is now -0.075656145402863 .
2024-07-10 20:47:32.193681 INFO::ASW Label was 0.465010085400402 prior to batch effect correction and is now 0.794167436567838 .
2024-07-10 20:47:32.194446 INFO::Total function execution time is 0.134973049163818 s and adjustment time is 0.118875503540039 s ( 88.07 )
2024-07-10 20:47:32.207083 INFO::Formatting Data.
2024-07-10 20:47:32.207762 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.208663 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.209639 INFO::Found 0 missing values.
2024-07-10 20:47:32.212247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.212755 INFO::Done
2024-07-10 20:47:32.21325 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.216076 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.216747 INFO::Found 2 batches.
2024-07-10 20:47:32.217279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.217859 INFO::Using default BPPARAM
2024-07-10 20:47:32.218378 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:32.21927 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:32.233136 INFO::Done
2024-07-10 20:47:32.233723 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.236441 INFO::ASW Batch was 0.698127076696058 prior to batch effect correction and is now 0.108702893225961 .
2024-07-10 20:47:32.236975 INFO::ASW Label was 0.397813317108167 prior to batch effect correction and is now 0.827218407779927 .
2024-07-10 20:47:32.237705 INFO::Total function execution time is 0.0306887626647949 s and adjustment time is 0.0165283679962158 s ( 53.86 )
2024-07-10 20:47:32.238468 INFO::Formatting Data.
2024-07-10 20:47:32.239051 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.239879 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.240792 INFO::Found 0 missing values.
2024-07-10 20:47:32.243265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.243781 INFO::Done
2024-07-10 20:47:32.244296 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.246994 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.247665 INFO::Found 2 batches.
2024-07-10 20:47:32.248189 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.248794 INFO::Using default BPPARAM
2024-07-10 20:47:32.249304 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:32.250165 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:32.26415 INFO::Done
2024-07-10 20:47:32.26474 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.267481 INFO::ASW Batch was 0.698127076696058 prior to batch effect correction and is now 0.108702893225961 .
2024-07-10 20:47:32.268044 INFO::ASW Label was 0.397813317108167 prior to batch effect correction and is now 0.827218407779927 .
2024-07-10 20:47:32.268776 INFO::Total function execution time is 0.0303196907043457 s and adjustment time is 0.0166256427764893 s ( 54.83 )
2024-07-10 20:47:32.279137 INFO::Formatting Data.
2024-07-10 20:47:32.279775 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.28063 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.281481 INFO::Found 0 missing values.
2024-07-10 20:47:32.28347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.284019 INFO::Done
2024-07-10 20:47:32.284524 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.286264 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.286985 INFO::Found 2 batches.
2024-07-10 20:47:32.287497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.288084 INFO::Using default BPPARAM
2024-07-10 20:47:32.288576 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:32.289423 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:32.340538 INFO::Done
2024-07-10 20:47:32.341203 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.343055 INFO::ASW Batch was -0.0859596784602841 prior to batch effect correction and is now -0.161423077540345 .
2024-07-10 20:47:32.343822 INFO::Total function execution time is 0.0647079944610596 s and adjustment time is 0.0537347793579102 s ( 83.04 )
2024-07-10 20:47:32.355224 INFO::Formatting Data.
2024-07-10 20:47:32.355939 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.356781 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.357763 INFO::Found 0 missing values.
2024-07-10 20:47:32.358921 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.
2024-07-10 20:47:32.363741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.364288 INFO::Done
2024-07-10 20:47:32.364792 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.3677 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.368371 INFO::Found 2 batches.
2024-07-10 20:47:32.368874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.369461 INFO::Using default BPPARAM
2024-07-10 20:47:32.369958 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:32.370981 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:32.387515 INFO::Done
2024-07-10 20:47:32.388155 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.391015 INFO::ASW Batch was 0.626580738520731 prior to batch effect correction and is now 0.0102060783440486 .
2024-07-10 20:47:32.391557 INFO::ASW Label was 0.445662251228538 prior to batch effect correction and is now 0.887188978201391 .
2024-07-10 20:47:32.392276 INFO::Total function execution time is 0.0370924472808838 s and adjustment time is 0.0192792415618896 s ( 51.98 )
2024-07-10 20:47:32.393071 INFO::Formatting Data.
2024-07-10 20:47:32.393679 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.39453 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.395475 INFO::Found 0 missing values.
2024-07-10 20:47:32.396362 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.
2024-07-10 20:47:32.403433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.404082 INFO::Done
2024-07-10 20:47:32.404674 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.407932 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.408649 INFO::Found 2 batches.
2024-07-10 20:47:32.409175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.409814 INFO::Using default BPPARAM
2024-07-10 20:47:32.410371 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:32.411382 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:32.429812 INFO::Done
2024-07-10 20:47:32.430562 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.433874 INFO::ASW Batch was 0.626580738520731 prior to batch effect correction and is now 0.0102060783440486 .
2024-07-10 20:47:32.434488 INFO::ASW Label was 0.445662251228538 prior to batch effect correction and is now 0.887188978201391 .
2024-07-10 20:47:32.435338 INFO::Total function execution time is 0.042264461517334 s and adjustment time is 0.0212969779968262 s ( 50.39 )
2024-07-10 20:47:32.646037 INFO::Formatting Data.
2024-07-10 20:47:32.64681 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.647676 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.64875 INFO::Found 0 missing values.
2024-07-10 20:47:32.651739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.652269 INFO::Done
2024-07-10 20:47:32.652796 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.654729 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.655421 INFO::Found 3 batches.
2024-07-10 20:47:32.655935 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.656548 INFO::Using default BPPARAM
2024-07-10 20:47:32.657111 INFO::Processing subtree level 1
2024-07-10 20:47:32.743304 INFO::Adjusting the last 1 batches sequentially
2024-07-10 20:47:32.745114 INFO::Done
2024-07-10 20:47:32.745753 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.748417 INFO::ASW Batch was -0.115451075882477 prior to batch effect correction and is now -0.115451075882477 .
2024-07-10 20:47:32.749381 INFO::Total function execution time is 0.103342771530151 s and adjustment time is 0.0898237228393555 s ( 86.92 )
2024-07-10 20:47:32.750508 INFO::Formatting Data.
2024-07-10 20:47:32.751156 INFO::Typecasting input to dataframe.
2024-07-10 20:47:32.751925 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.752844 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.753935 INFO::Found 0 missing values.
2024-07-10 20:47:32.756886 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.757433 INFO::Done
2024-07-10 20:47:32.757981 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.759938 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.760615 INFO::Found 3 batches.
2024-07-10 20:47:32.761148 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.761766 INFO::Using default BPPARAM
2024-07-10 20:47:32.762279 INFO::Processing subtree level 1
2024-07-10 20:47:32.847692 INFO::Adjusting the last 1 batches sequentially
2024-07-10 20:47:32.849399 INFO::Done
2024-07-10 20:47:32.850015 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.852399 INFO::ASW Batch was -0.115451075882477 prior to batch effect correction and is now -0.115451075882477 .
2024-07-10 20:47:32.853311 INFO::Total function execution time is 0.10279369354248 s and adjustment time is 0.0889041423797607 s ( 86.49 )
2024-07-10 20:47:32.865407 INFO::Formatting Data.
2024-07-10 20:47:32.866165 INFO::Typecasting input to dataframe.
2024-07-10 20:47:32.866992 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:32.867871 INFO::Removing potential empty rows and columns
2024-07-10 20:47:32.868902 INFO::Found 0 missing values.
2024-07-10 20:47:32.871843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:32.872361 INFO::Done
2024-07-10 20:47:32.872864 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:32.874944 INFO::Starting hierarchical adjustment
2024-07-10 20:47:32.875724 INFO::Found 3 batches.
2024-07-10 20:47:32.876285 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:32.876894 INFO::Using default BPPARAM
2024-07-10 20:47:32.877444 INFO::Processing subtree level 1
2024-07-10 20:47:32.966398 INFO::Adjusting the last 1 batches sequentially
2024-07-10 20:47:32.968071 INFO::Done
2024-07-10 20:47:32.968695 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:32.971087 INFO::ASW Batch was -0.0380187045114157 prior to batch effect correction and is now -0.0380187045114157 .
2024-07-10 20:47:32.971993 INFO::Total function execution time is 0.10660195350647 s and adjustment time is 0.0924897193908691 s ( 86.76 )
2024-07-10 20:47:33.133991 INFO::Formatting Data.
2024-07-10 20:47:33.134878 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:33.136086 INFO::Removing potential empty rows and columns
2024-07-10 20:47:33.139003 INFO::Found 1000 missing values.
2024-07-10 20:47:33.158659 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:33.159517 INFO::Done
2024-07-10 20:47:33.16016 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:33.166079 INFO::Starting hierarchical adjustment
2024-07-10 20:47:33.166903 INFO::Found 10 batches.
2024-07-10 20:47:33.167473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:33.168192 INFO::Using default BPPARAM
2024-07-10 20:47:33.168757 INFO::Processing subtree level 1
2024-07-10 20:47:33.377909 INFO::Processing subtree level 2
2024-07-10 20:47:33.591069 INFO::Adjusting the last 1 batches sequentially
2024-07-10 20:47:33.59332 INFO::Done
2024-07-10 20:47:33.594093 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:33.601115 INFO::ASW Batch was 0.401983486564559 prior to batch effect correction and is now 0.401983486564559 .
2024-07-10 20:47:33.601939 INFO::ASW Label was 0.386400899012745 prior to batch effect correction and is now 0.386400899012745 .
2024-07-10 20:47:33.602998 INFO::Total function execution time is 0.469048500061035 s and adjustment time is 0.4265456199646 s ( 90.94 )
2024-07-10 20:47:33.603954 INFO::Formatting Data.
2024-07-10 20:47:33.604691 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:33.60627 INFO::Removing potential empty rows and columns
2024-07-10 20:47:33.609823 INFO::Found 1000 missing values.
2024-07-10 20:47:33.651754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:33.65258 INFO::Done
2024-07-10 20:47:33.653153 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:33.658871 INFO::Starting hierarchical adjustment
2024-07-10 20:47:33.659723 INFO::Found 10 batches.
2024-07-10 20:47:34.687472 INFO::Set up parallel execution backend with 2 workers
2024-07-10 20:47:34.688755 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-10 20:47:35.908366 INFO::Adjusting the last 2 batches sequentially
2024-07-10 20:47:35.909704 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-10 20:47:35.924677 INFO::Done
2024-07-10 20:47:35.925252 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:35.929702 INFO::ASW Batch was 0.401983486564559 prior to batch effect correction and is now 0.401983486564559 .
2024-07-10 20:47:35.930222 INFO::ASW Label was 0.386400899012745 prior to batch effect correction and is now 0.386400899012745 .
2024-07-10 20:47:35.930961 INFO::Total function execution time is 2.32707691192627 s and adjustment time is 2.26513338088989 s ( 97.34 )
2024-07-10 20:47:36.056623 INFO::Formatting Data.
2024-07-10 20:47:36.057418 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.058362 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.059399 INFO::Found 0 missing values.
2024-07-10 20:47:36.062804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.063349 INFO::Done
2024-07-10 20:47:36.063865 INFO::Acquiring quality metrics before batch effect correction.
2024-07-10 20:47:36.066417 INFO::Starting hierarchical adjustment
2024-07-10 20:47:36.067063 INFO::Found 3 batches.
2024-07-10 20:47:36.067557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-10 20:47:36.068137 INFO::Using default BPPARAM
2024-07-10 20:47:36.068628 INFO::Processing subtree level 1
2024-07-10 20:47:36.16072 INFO::Adjusting the last 1 batches sequentially
2024-07-10 20:47:36.162363 INFO::Done
2024-07-10 20:47:36.162967 INFO::Acquiring quality metrics after batch effect correction.
2024-07-10 20:47:36.165967 INFO::ASW Batch was 0.109034160338068 prior to batch effect correction and is now -0.134033548661156 .
2024-07-10 20:47:36.166564 INFO::ASW Label was -0.164522682655826 prior to batch effect correction and is now -0.0493752473065533 .
2024-07-10 20:47:36.167388 INFO::Total function execution time is 0.110848903656006 s and adjustment time is 0.0954232215881348 s ( 86.08 )
2024-07-10 20:47:36.27973 INFO::Formatting Data.
2024-07-10 20:47:36.280552 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.28142 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.282445 INFO::Found 2 missing values.
2024-07-10 20:47:36.285314 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.285828 INFO::Done
2024-07-10 20:47:36.311223 INFO::Found NA in Reference column
2024-07-10 20:47:36.320655 INFO::Require at least two references per batch.
2024-07-10 20:47:36.340295 INFO::Formatting Data.
2024-07-10 20:47:36.341064 INFO::Recognized SummarizedExperiment
2024-07-10 20:47:36.341635 INFO::Typecasting input to dataframe.
2024-07-10 20:47:36.351044 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.352231 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.355882 INFO::Found 0 missing values.
2024-07-10 20:47:36.362664 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.363302 INFO::Done
2024-07-10 20:47:36.377731 INFO::Formatting Data.
2024-07-10 20:47:36.378431 INFO::Recognized SummarizedExperiment
2024-07-10 20:47:36.378935 INFO::Typecasting input to dataframe.
2024-07-10 20:47:36.39482 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.396024 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.3993 INFO::Found 0 missing values.
2024-07-10 20:47:36.409339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.410019 INFO::Done
2024-07-10 20:47:36.424391 INFO::Formatting Data.
2024-07-10 20:47:36.425097 INFO::Recognized SummarizedExperiment
2024-07-10 20:47:36.42563 INFO::Typecasting input to dataframe.
2024-07-10 20:47:36.440732 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.441659 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.442654 INFO::Found 0 missing values.
2024-07-10 20:47:36.443644 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.
2024-07-10 20:47:36.447908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.448421 INFO::Done
2024-07-10 20:47:36.457816 INFO::Formatting Data.
2024-07-10 20:47:36.458538 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.459363 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.460517 INFO::Found 0 missing values.
2024-07-10 20:47:36.463427 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.463946 INFO::Done
2024-07-10 20:47:36.473882 INFO::Formatting Data.
2024-07-10 20:47:36.474579 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.475424 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.47643 INFO::Found 0 missing values.
2024-07-10 20:47:36.479155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.47969 INFO::Done
2024-07-10 20:47:36.505349 INFO::Formatting Data.
2024-07-10 20:47:36.506096 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.507044 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.508132 INFO::Found 1 missing values.
2024-07-10 20:47:36.510469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.510962 INFO::Done
2024-07-10 20:47:36.527459 INFO::Formatting Data.
2024-07-10 20:47:36.528257 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.529095 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.530037 INFO::Found 2 missing values.
2024-07-10 20:47:36.530888 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.
2024-07-10 20:47:36.533042 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.533579 INFO::Done
2024-07-10 20:47:36.542425 INFO::Formatting Data.
2024-07-10 20:47:36.54308 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.543892 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.54478 INFO::Found 2 missing values.
2024-07-10 20:47:36.546283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.546788 INFO::Done
2024-07-10 20:47:36.55613 INFO::Formatting Data.
2024-07-10 20:47:36.556848 INFO::Typecasting input to dataframe.
2024-07-10 20:47:36.557662 INFO::Replacing NaNs with NAs.
2024-07-10 20:47:36.558481 INFO::Removing potential empty rows and columns
2024-07-10 20:47:36.559467 INFO::Found 0 missing values.
2024-07-10 20:47:36.56232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-10 20:47:36.562846 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.134 3.507 19.172
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.424 | 1.590 | 17.885 | |
| compute_asw | 0.026 | 0.000 | 0.026 | |
| count_existing | 0.015 | 0.000 | 0.015 | |
| generate_data_covariables | 0.010 | 0.004 | 0.013 | |
| generate_dataset | 0.013 | 0.000 | 0.012 | |