Yannis Schumann
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 2024-06-11 14:39 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| 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: 2024-06-09 20:48:56 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 20:50:25 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 89.2 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 4.4.0 (2024-04-24)
* 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 25.593 1.317 18.529
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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")
2024-06-09 20:49:48.899403 INFO::Formatting Data.
2024-06-09 20:49:48.900931 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:48.91201 INFO::Removing potential empty rows and columns
2024-06-09 20:49:49.152567 INFO::Found 0 missing values.
2024-06-09 20:49:49.155709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:49.156289 INFO::Done
2024-06-09 20:49:49.15679 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:49.168688 INFO::Starting hierarchical adjustment
2024-06-09 20:49:49.169627 INFO::Found 3 batches.
2024-06-09 20:49:49.170164 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:49.1713 INFO::Using default BPPARAM
2024-06-09 20:49:49.171829 INFO::Processing subtree level 1
2024-06-09 20:49:49.261803 INFO::Adjusting the last 1 batches sequentially
2024-06-09 20:49:49.263687 INFO::Done
2024-06-09 20:49:49.264359 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:49.266865 INFO::ASW Batch was -0.091572838932462 prior to batch effect correction and is now -0.091572838932462 .
2024-06-09 20:49:49.26798 INFO::Total function execution time is 0.369482755661011 s and adjustment time is 0.094240665435791 s ( 25.51 )
2024-06-09 20:49:49.282084 INFO::Formatting Data.
2024-06-09 20:49:49.282922 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:49.283858 INFO::Removing potential empty rows and columns
2024-06-09 20:49:49.284964 INFO::Found 0 missing values.
2024-06-09 20:49:49.285921 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-09 20:49:49.29721 INFO::Formatting Data.
2024-06-09 20:49:49.298041 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:49.298959 INFO::Removing potential empty rows and columns
2024-06-09 20:49:49.300017 INFO::Found 0 missing values.
2024-06-09 20:49:49.300925 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-09 20:49:49.3167 INFO::Formatting Data.
2024-06-09 20:49:49.31745 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:49.318316 INFO::Removing potential empty rows and columns
2024-06-09 20:49:49.31931 INFO::Found 0 missing values.
2024-06-09 20:49:49.320165 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-09 20:49:49.324289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:49.3248 INFO::Done
2024-06-09 20:49:49.325292 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:49.327226 INFO::Starting hierarchical adjustment
2024-06-09 20:49:49.327888 INFO::Found 2 batches.
2024-06-09 20:49:49.328394 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:49.32899 INFO::Using default BPPARAM
2024-06-09 20:49:49.329488 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:49.330362 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:49.351011 INFO::Done
2024-06-09 20:49:49.351679 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:49.353584 INFO::ASW Batch was -0.0327247653315646 prior to batch effect correction and is now -0.113847527270036 .
2024-06-09 20:49:49.354346 INFO::Total function execution time is 0.0377209186553955 s and adjustment time is 0.0232257843017578 s ( 61.57 )
2024-06-09 20:49:49.356954 INFO::Formatting Data.
2024-06-09 20:49:49.357544 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:49.365751 INFO::Formatting Data.
2024-06-09 20:49:49.366432 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:49.367268 INFO::Removing potential empty rows and columns
2024-06-09 20:49:49.368225 INFO::Found 0 missing values.
2024-06-09 20:49:49.370914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:49.371407 INFO::Done
2024-06-09 20:49:49.371895 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:49.373742 INFO::Starting hierarchical adjustment
2024-06-09 20:49:49.374402 INFO::Found 2 batches.
2024-06-09 20:49:49.374915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:49.375472 INFO::Using default BPPARAM
2024-06-09 20:49:49.375979 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:49.376816 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:49.391599 INFO::Done
2024-06-09 20:49:49.392288 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:49.394289 INFO::ASW Batch was 0.0288892645619594 prior to batch effect correction and is now -0.115238792076715 .
2024-06-09 20:49:49.395095 INFO::Total function execution time is 0.0293822288513184 s and adjustment time is 0.0173051357269287 s ( 58.9 )
2024-06-09 20:49:49.396176 INFO::Formatting Data.
2024-06-09 20:49:49.396747 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:49.397583 INFO::Removing potential empty rows and columns
2024-06-09 20:49:49.398591 INFO::Found 0 missing values.
2024-06-09 20:49:49.401361 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:49.401867 INFO::Done
2024-06-09 20:49:49.402355 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:49.40438 INFO::Starting hierarchical adjustment
2024-06-09 20:49:49.40505 INFO::Found 2 batches.
2024-06-09 20:49:49.405539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:49.406104 INFO::Using default BPPARAM
2024-06-09 20:49:49.406594 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:49.40747 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:49.422023 INFO::Done
2024-06-09 20:49:49.422745 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:49.424757 INFO::ASW Batch was 0.0288892645619594 prior to batch effect correction and is now -0.115238792076715 .
2024-06-09 20:49:49.425515 INFO::Total function execution time is 0.0293443202972412 s and adjustment time is 0.0170862674713135 s ( 58.23 )
2024-06-09 20:49:51.616992 INFO::Formatting Data.
2024-06-09 20:49:51.617781 INFO::Recognized SummarizedExperiment
2024-06-09 20:49:51.6183 INFO::Typecasting input to dataframe.
2024-06-09 20:49:51.650257 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:51.651465 INFO::Removing potential empty rows and columns
2024-06-09 20:49:51.655172 INFO::Found 0 missing values.
2024-06-09 20:49:51.660918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:51.661469 INFO::Done
2024-06-09 20:49:51.661922 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:51.665051 INFO::Starting hierarchical adjustment
2024-06-09 20:49:51.665665 INFO::Found 2 batches.
2024-06-09 20:49:51.666105 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:51.667094 INFO::Using default BPPARAM
2024-06-09 20:49:51.667554 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:51.668406 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:51.767189 INFO::Done
2024-06-09 20:49:51.767936 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:51.77127 INFO::ASW Batch was 0.021288835587915 prior to batch effect correction and is now -0.0927039259033276 .
2024-06-09 20:49:51.772106 INFO::Total function execution time is 0.155445575714111 s and adjustment time is 0.101602554321289 s ( 65.36 )
2024-06-09 20:49:51.788096 INFO::Formatting Data.
2024-06-09 20:49:51.78877 INFO::Recognized SummarizedExperiment
2024-06-09 20:49:51.789251 INFO::Typecasting input to dataframe.
2024-06-09 20:49:51.797524 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:51.798602 INFO::Removing potential empty rows and columns
2024-06-09 20:49:51.801787 INFO::Found 0 missing values.
2024-06-09 20:49:51.807868 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:51.808439 INFO::Done
2024-06-09 20:49:51.808916 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:51.811949 INFO::Starting hierarchical adjustment
2024-06-09 20:49:51.812618 INFO::Found 2 batches.
2024-06-09 20:49:51.813083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:51.813615 INFO::Using default BPPARAM
2024-06-09 20:49:51.814082 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:51.815048 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:51.836728 INFO::Done
2024-06-09 20:49:51.837401 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:51.84065 INFO::ASW Batch was 0.00439443858001584 prior to batch effect correction and is now 0.00439443858001584 .
2024-06-09 20:49:51.84145 INFO::Total function execution time is 0.053330659866333 s and adjustment time is 0.0242092609405518 s ( 45.39 )
2024-06-09 20:49:51.857448 INFO::Formatting Data.
2024-06-09 20:49:51.858175 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:51.858995 INFO::Removing potential empty rows and columns
2024-06-09 20:49:51.85991 INFO::Found 0 missing values.
2024-06-09 20:49:51.862467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:51.862962 INFO::Done
2024-06-09 20:49:51.86342 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:51.865138 INFO::Starting hierarchical adjustment
2024-06-09 20:49:51.865764 INFO::Found 3 batches.
2024-06-09 20:49:51.866234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:51.866812 INFO::Using default BPPARAM
2024-06-09 20:49:51.867282 INFO::Processing subtree level 1
2024-06-09 20:49:52.031516 INFO::Adjusting the last 1 batches sequentially
2024-06-09 20:49:52.033578 INFO::Done
2024-06-09 20:49:52.034315 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:52.037222 INFO::ASW Batch was 0.0047372760662203 prior to batch effect correction and is now -0.154417680494542 .
2024-06-09 20:49:52.038314 INFO::Total function execution time is 0.180850028991699 s and adjustment time is 0.167892217636108 s ( 92.84 )
2024-06-09 20:49:52.055777 INFO::Skipping initial DF formatting
2024-06-09 20:49:52.056621 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:52.061269 INFO::Starting hierarchical adjustment
2024-06-09 20:49:52.062103 INFO::Found 5 batches.
2024-06-09 20:49:52.062643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:52.063278 INFO::Using default BPPARAM
2024-06-09 20:49:52.063843 INFO::Processing subtree level 1
2024-06-09 20:49:52.241718 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:52.243668 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:52.266405 INFO::Done
2024-06-09 20:49:52.267184 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:52.271584 INFO::ASW Batch was 0.482835530436282 prior to batch effect correction and is now 0.482835530436282 .
2024-06-09 20:49:52.272296 INFO::ASW Label was 0.380801112389743 prior to batch effect correction and is now 0.380801112389743 .
2024-06-09 20:49:52.273368 INFO::Total function execution time is 0.21766996383667 s and adjustment time is 0.204442501068115 s ( 93.92 )
2024-06-09 20:49:52.291619 INFO::Formatting Data.
2024-06-09 20:49:52.292455 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:52.293374 INFO::Removing potential empty rows and columns
2024-06-09 20:49:52.29438 INFO::Found 0 missing values.
2024-06-09 20:49:52.301518 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:52.302166 INFO::Done
2024-06-09 20:49:52.302756 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:52.305921 INFO::Starting hierarchical adjustment
2024-06-09 20:49:52.306666 INFO::Found 5 batches.
2024-06-09 20:49:52.307195 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:52.30782 INFO::Using default BPPARAM
2024-06-09 20:49:52.308385 INFO::Processing subtree level 1
2024-06-09 20:49:52.415437 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:52.417086 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:52.432705 INFO::Done
2024-06-09 20:49:52.433419 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:52.436479 INFO::ASW Batch was 0.483220298893193 prior to batch effect correction and is now -0.0246506567972269 .
2024-06-09 20:49:52.437045 INFO::ASW Label was 0.348266536727909 prior to batch effect correction and is now 0.809744692263564 .
2024-06-09 20:49:52.437864 INFO::Total function execution time is 0.146383762359619 s and adjustment time is 0.126177072525024 s ( 86.2 )
2024-06-09 20:49:52.438659 INFO::Formatting Data.
2024-06-09 20:49:52.439244 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:52.440074 INFO::Removing potential empty rows and columns
2024-06-09 20:49:52.440973 INFO::Found 0 missing values.
2024-06-09 20:49:52.444855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:52.445418 INFO::Done
2024-06-09 20:49:52.445921 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:52.448847 INFO::Starting hierarchical adjustment
2024-06-09 20:49:52.449518 INFO::Found 5 batches.
2024-06-09 20:49:52.450038 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:52.450649 INFO::Using default BPPARAM
2024-06-09 20:49:52.451182 INFO::Processing subtree level 1
2024-06-09 20:49:52.589272 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:52.591238 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:52.608368 INFO::Done
2024-06-09 20:49:52.609223 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:52.612525 INFO::ASW Batch was 0.483220298893193 prior to batch effect correction and is now -0.0246506567972269 .
2024-06-09 20:49:52.613215 INFO::ASW Label was 0.348266536727909 prior to batch effect correction and is now 0.809744692263564 .
2024-06-09 20:49:52.614071 INFO::Total function execution time is 0.175389528274536 s and adjustment time is 0.158936262130737 s ( 90.62 )
2024-06-09 20:49:52.627117 INFO::Formatting Data.
2024-06-09 20:49:52.62792 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:52.628828 INFO::Removing potential empty rows and columns
2024-06-09 20:49:52.629816 INFO::Found 0 missing values.
2024-06-09 20:49:52.633881 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:52.634433 INFO::Done
2024-06-09 20:49:52.634988 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:52.638037 INFO::Starting hierarchical adjustment
2024-06-09 20:49:52.63877 INFO::Found 5 batches.
2024-06-09 20:49:52.639297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:52.639903 INFO::Using default BPPARAM
2024-06-09 20:49:52.640459 INFO::Processing subtree level 1
2024-06-09 20:49:52.768943 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:52.771051 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:52.787775 INFO::Done
2024-06-09 20:49:52.788512 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:52.791821 INFO::ASW Batch was 0.491344740479147 prior to batch effect correction and is now -0.057065643877568 .
2024-06-09 20:49:52.792459 INFO::ASW Label was 0.222690372887857 prior to batch effect correction and is now 0.797385594361485 .
2024-06-09 20:49:52.79336 INFO::Total function execution time is 0.166300296783447 s and adjustment time is 0.149129867553711 s ( 89.68 )
2024-06-09 20:49:52.79427 INFO::Formatting Data.
2024-06-09 20:49:52.794965 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:52.795888 INFO::Removing potential empty rows and columns
2024-06-09 20:49:52.797007 INFO::Found 0 missing values.
2024-06-09 20:49:52.801144 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:52.801705 INFO::Done
2024-06-09 20:49:52.802225 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:52.805266 INFO::Starting hierarchical adjustment
2024-06-09 20:49:52.805987 INFO::Found 5 batches.
2024-06-09 20:49:52.806504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:52.807133 INFO::Using default BPPARAM
2024-06-09 20:49:52.80766 INFO::Processing subtree level 1
2024-06-09 20:49:52.935822 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:52.937941 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:52.954372 INFO::Done
2024-06-09 20:49:52.955149 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:52.958428 INFO::ASW Batch was 0.491344740479147 prior to batch effect correction and is now -0.057065643877568 .
2024-06-09 20:49:52.959115 INFO::ASW Label was 0.222690372887857 prior to batch effect correction and is now 0.797385594361485 .
2024-06-09 20:49:52.960052 INFO::Total function execution time is 0.165775060653687 s and adjustment time is 0.148487329483032 s ( 89.57 )
2024-06-09 20:49:52.97829 INFO::Formatting Data.
2024-06-09 20:49:52.979343 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:52.98034 INFO::Removing potential empty rows and columns
2024-06-09 20:49:52.981425 INFO::Found 0 missing values.
2024-06-09 20:49:52.984218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:52.984771 INFO::Done
2024-06-09 20:49:52.985282 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:52.988543 INFO::Starting hierarchical adjustment
2024-06-09 20:49:52.989261 INFO::Found 2 batches.
2024-06-09 20:49:52.989795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:52.990473 INFO::Using default BPPARAM
2024-06-09 20:49:52.991062 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:52.991963 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:53.007701 INFO::Done
2024-06-09 20:49:53.008412 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.011429 INFO::ASW Batch was 0.608998627284364 prior to batch effect correction and is now 0.0774025684139695 .
2024-06-09 20:49:53.012039 INFO::ASW Label was 0.492749792173181 prior to batch effect correction and is now 0.839448299628386 .
2024-06-09 20:49:53.012851 INFO::Total function execution time is 0.0349221229553223 s and adjustment time is 0.0185830593109131 s ( 53.21 )
2024-06-09 20:49:53.013665 INFO::Formatting Data.
2024-06-09 20:49:53.014276 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.015144 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.016092 INFO::Found 0 missing values.
2024-06-09 20:49:53.018704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.01926 INFO::Done
2024-06-09 20:49:53.019758 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.022761 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.023461 INFO::Found 2 batches.
2024-06-09 20:49:53.023977 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.024564 INFO::Using default BPPARAM
2024-06-09 20:49:53.025103 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:53.026019 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:53.040725 INFO::Done
2024-06-09 20:49:53.041374 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.044278 INFO::ASW Batch was 0.608998627284364 prior to batch effect correction and is now 0.0774025684139695 .
2024-06-09 20:49:53.044843 INFO::ASW Label was 0.492749792173181 prior to batch effect correction and is now 0.839448299628386 .
2024-06-09 20:49:53.045631 INFO::Total function execution time is 0.0319695472717285 s and adjustment time is 0.0174198150634766 s ( 54.49 )
2024-06-09 20:49:53.05699 INFO::Formatting Data.
2024-06-09 20:49:53.057744 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.058632 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.059513 INFO::Found 0 missing values.
2024-06-09 20:49:53.061537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.062056 INFO::Done
2024-06-09 20:49:53.062597 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.06449 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.065193 INFO::Found 2 batches.
2024-06-09 20:49:53.065712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.066331 INFO::Using default BPPARAM
2024-06-09 20:49:53.066862 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:53.067759 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:53.100324 INFO::Done
2024-06-09 20:49:53.101022 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.103031 INFO::ASW Batch was -0.0772232998051518 prior to batch effect correction and is now -0.13008339114839 .
2024-06-09 20:49:53.103854 INFO::Total function execution time is 0.0469198226928711 s and adjustment time is 0.0352394580841064 s ( 75.11 )
2024-06-09 20:49:53.115534 INFO::Formatting Data.
2024-06-09 20:49:53.116339 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.117238 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.118237 INFO::Found 0 missing values.
2024-06-09 20:49:53.119529 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-09 20:49:53.150031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.150766 INFO::Done
2024-06-09 20:49:53.151307 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.154162 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.154895 INFO::Found 2 batches.
2024-06-09 20:49:53.155418 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.155982 INFO::Using default BPPARAM
2024-06-09 20:49:53.156483 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:53.157483 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:53.174228 INFO::Done
2024-06-09 20:49:53.174918 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.177828 INFO::ASW Batch was 0.465693863825874 prior to batch effect correction and is now 0.100767211457926 .
2024-06-09 20:49:53.178377 INFO::ASW Label was 0.626867844583166 prior to batch effect correction and is now 0.858021970250488 .
2024-06-09 20:49:53.179129 INFO::Total function execution time is 0.0636899471282959 s and adjustment time is 0.0194644927978516 s ( 30.56 )
2024-06-09 20:49:53.179883 INFO::Formatting Data.
2024-06-09 20:49:53.180462 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.181354 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.182322 INFO::Found 0 missing values.
2024-06-09 20:49:53.183248 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-09 20:49:53.188035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.188569 INFO::Done
2024-06-09 20:49:53.18907 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.192136 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.192823 INFO::Found 2 batches.
2024-06-09 20:49:53.193348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.193959 INFO::Using default BPPARAM
2024-06-09 20:49:53.194464 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:53.195432 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:53.212521 INFO::Done
2024-06-09 20:49:53.213196 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.216152 INFO::ASW Batch was 0.465693863825874 prior to batch effect correction and is now 0.100767211457926 .
2024-06-09 20:49:53.216709 INFO::ASW Label was 0.626867844583166 prior to batch effect correction and is now 0.858021970250488 .
2024-06-09 20:49:53.217491 INFO::Total function execution time is 0.0376186370849609 s and adjustment time is 0.0198380947113037 s ( 52.73 )
2024-06-09 20:49:53.454682 INFO::Formatting Data.
2024-06-09 20:49:53.455681 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.456646 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.457716 INFO::Found 0 missing values.
2024-06-09 20:49:53.460749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.461312 INFO::Done
2024-06-09 20:49:53.461823 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.464102 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.464841 INFO::Found 3 batches.
2024-06-09 20:49:53.465372 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.465997 INFO::Using default BPPARAM
2024-06-09 20:49:53.466535 INFO::Processing subtree level 1
2024-06-09 20:49:53.557645 INFO::Adjusting the last 1 batches sequentially
2024-06-09 20:49:53.559354 INFO::Done
2024-06-09 20:49:53.559979 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.562374 INFO::ASW Batch was -0.0804625092032904 prior to batch effect correction and is now -0.0804625092032904 .
2024-06-09 20:49:53.563352 INFO::Total function execution time is 0.108820676803589 s and adjustment time is 0.0947036743164062 s ( 87.03 )
2024-06-09 20:49:53.564533 INFO::Formatting Data.
2024-06-09 20:49:53.565203 INFO::Typecasting input to dataframe.
2024-06-09 20:49:53.56598 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.566954 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.568048 INFO::Found 0 missing values.
2024-06-09 20:49:53.57114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.571697 INFO::Done
2024-06-09 20:49:53.572224 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.574236 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.575034 INFO::Found 3 batches.
2024-06-09 20:49:53.575636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.576289 INFO::Using default BPPARAM
2024-06-09 20:49:53.576824 INFO::Processing subtree level 1
2024-06-09 20:49:53.664921 INFO::Adjusting the last 1 batches sequentially
2024-06-09 20:49:53.666642 INFO::Done
2024-06-09 20:49:53.667255 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.669592 INFO::ASW Batch was -0.0804625092032904 prior to batch effect correction and is now -0.0804625092032904 .
2024-06-09 20:49:53.670501 INFO::Total function execution time is 0.105961561203003 s and adjustment time is 0.0917673110961914 s ( 86.6 )
2024-06-09 20:49:53.682713 INFO::Formatting Data.
2024-06-09 20:49:53.683462 INFO::Typecasting input to dataframe.
2024-06-09 20:49:53.684301 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.685169 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.686242 INFO::Found 0 missing values.
2024-06-09 20:49:53.689259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.689789 INFO::Done
2024-06-09 20:49:53.690302 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.69224 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.692944 INFO::Found 3 batches.
2024-06-09 20:49:53.693453 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.69404 INFO::Using default BPPARAM
2024-06-09 20:49:53.694565 INFO::Processing subtree level 1
2024-06-09 20:49:53.779758 INFO::Adjusting the last 1 batches sequentially
2024-06-09 20:49:53.781414 INFO::Done
2024-06-09 20:49:53.782 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:53.784358 INFO::ASW Batch was 0.0276460236934886 prior to batch effect correction and is now 0.0276460236934886 .
2024-06-09 20:49:53.785239 INFO::Total function execution time is 0.102596044540405 s and adjustment time is 0.0886015892028809 s ( 86.36 )
2024-06-09 20:49:53.919403 INFO::Formatting Data.
2024-06-09 20:49:53.920215 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:53.921325 INFO::Removing potential empty rows and columns
2024-06-09 20:49:53.924093 INFO::Found 1000 missing values.
2024-06-09 20:49:53.94195 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:53.942672 INFO::Done
2024-06-09 20:49:53.943244 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:53.94894 INFO::Starting hierarchical adjustment
2024-06-09 20:49:53.949649 INFO::Found 10 batches.
2024-06-09 20:49:53.950158 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:53.950768 INFO::Using default BPPARAM
2024-06-09 20:49:53.951307 INFO::Processing subtree level 1
2024-06-09 20:49:54.095833 INFO::Processing subtree level 2
2024-06-09 20:49:54.316085 INFO::Adjusting the last 1 batches sequentially
2024-06-09 20:49:54.318274 INFO::Done
2024-06-09 20:49:54.319096 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:54.325366 INFO::ASW Batch was 0.468299189874964 prior to batch effect correction and is now 0.468299189874964 .
2024-06-09 20:49:54.326087 INFO::ASW Label was 0.34462268195728 prior to batch effect correction and is now 0.34462268195728 .
2024-06-09 20:49:54.327093 INFO::Total function execution time is 0.407751560211182 s and adjustment time is 0.368730783462524 s ( 90.43 )
2024-06-09 20:49:54.328012 INFO::Formatting Data.
2024-06-09 20:49:54.328714 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:54.329989 INFO::Removing potential empty rows and columns
2024-06-09 20:49:54.333237 INFO::Found 1000 missing values.
2024-06-09 20:49:54.35416 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:54.355082 INFO::Done
2024-06-09 20:49:54.355701 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:54.362534 INFO::Starting hierarchical adjustment
2024-06-09 20:49:54.363524 INFO::Found 10 batches.
2024-06-09 20:49:55.620805 INFO::Set up parallel execution backend with 2 workers
2024-06-09 20:49:55.622607 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-09 20:49:56.966538 INFO::Adjusting the last 2 batches sequentially
2024-06-09 20:49:56.968692 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 20:49:56.985134 INFO::Done
2024-06-09 20:49:56.985792 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:56.990636 INFO::ASW Batch was 0.468299189874964 prior to batch effect correction and is now 0.468299189874964 .
2024-06-09 20:49:56.991201 INFO::ASW Label was 0.34462268195728 prior to batch effect correction and is now 0.34462268195728 .
2024-06-09 20:49:56.991953 INFO::Total function execution time is 2.6639883518219 s and adjustment time is 2.62182569503784 s ( 98.42 )
2024-06-09 20:49:57.143182 INFO::Formatting Data.
2024-06-09 20:49:57.144155 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.145225 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.146457 INFO::Found 0 missing values.
2024-06-09 20:49:57.150384 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.151022 INFO::Done
2024-06-09 20:49:57.151582 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 20:49:57.15459 INFO::Starting hierarchical adjustment
2024-06-09 20:49:57.155336 INFO::Found 3 batches.
2024-06-09 20:49:57.155875 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 20:49:57.156525 INFO::Using default BPPARAM
2024-06-09 20:49:57.157076 INFO::Processing subtree level 1
2024-06-09 20:49:57.26498 INFO::Adjusting the last 1 batches sequentially
2024-06-09 20:49:57.267058 INFO::Done
2024-06-09 20:49:57.267757 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 20:49:57.271426 INFO::ASW Batch was 0.187357197754573 prior to batch effect correction and is now -0.158139062761375 .
2024-06-09 20:49:57.272082 INFO::ASW Label was -0.171184374451381 prior to batch effect correction and is now 0.0556707845371332 .
2024-06-09 20:49:57.273158 INFO::Total function execution time is 0.130043029785156 s and adjustment time is 0.11184024810791 s ( 86 )
2024-06-09 20:49:57.391387 INFO::Formatting Data.
2024-06-09 20:49:57.392257 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.393138 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.394148 INFO::Found 2 missing values.
2024-06-09 20:49:57.396882 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.39739 INFO::Done
2024-06-09 20:49:57.421914 INFO::Found NA in Reference column
2024-06-09 20:49:57.431172 INFO::Require at least two references per batch.
2024-06-09 20:49:57.450841 INFO::Formatting Data.
2024-06-09 20:49:57.451657 INFO::Recognized SummarizedExperiment
2024-06-09 20:49:57.452195 INFO::Typecasting input to dataframe.
2024-06-09 20:49:57.46159 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.4628 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.466197 INFO::Found 0 missing values.
2024-06-09 20:49:57.47276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.47339 INFO::Done
2024-06-09 20:49:57.489235 INFO::Formatting Data.
2024-06-09 20:49:57.490069 INFO::Recognized SummarizedExperiment
2024-06-09 20:49:57.490654 INFO::Typecasting input to dataframe.
2024-06-09 20:49:57.50892 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.5102 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.51394 INFO::Found 0 missing values.
2024-06-09 20:49:57.525561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.526339 INFO::Done
2024-06-09 20:49:57.547133 INFO::Formatting Data.
2024-06-09 20:49:57.54812 INFO::Recognized SummarizedExperiment
2024-06-09 20:49:57.54875 INFO::Typecasting input to dataframe.
2024-06-09 20:49:57.566482 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.567655 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.569041 INFO::Found 0 missing values.
2024-06-09 20:49:57.570122 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-09 20:49:57.575063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.575753 INFO::Done
2024-06-09 20:49:57.587271 INFO::Formatting Data.
2024-06-09 20:49:57.588202 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.589175 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.590453 INFO::Found 0 missing values.
2024-06-09 20:49:57.593638 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.594187 INFO::Done
2024-06-09 20:49:57.606375 INFO::Formatting Data.
2024-06-09 20:49:57.607237 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.608159 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.609207 INFO::Found 0 missing values.
2024-06-09 20:49:57.612177 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.61275 INFO::Done
2024-06-09 20:49:57.645164 INFO::Formatting Data.
2024-06-09 20:49:57.64624 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.647527 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.648866 INFO::Found 1 missing values.
2024-06-09 20:49:57.651932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.652568 INFO::Done
2024-06-09 20:49:57.674703 INFO::Formatting Data.
2024-06-09 20:49:57.675889 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.677025 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.678186 INFO::Found 2 missing values.
2024-06-09 20:49:57.679304 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-09 20:49:57.681905 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.682516 INFO::Done
2024-06-09 20:49:57.694267 INFO::Formatting Data.
2024-06-09 20:49:57.695206 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.69631 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.69744 INFO::Found 2 missing values.
2024-06-09 20:49:57.699576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.700175 INFO::Done
2024-06-09 20:49:57.712383 INFO::Formatting Data.
2024-06-09 20:49:57.713329 INFO::Typecasting input to dataframe.
2024-06-09 20:49:57.714344 INFO::Replacing NaNs with NAs.
2024-06-09 20:49:57.715404 INFO::Removing potential empty rows and columns
2024-06-09 20:49:57.716532 INFO::Found 0 missing values.
2024-06-09 20:49:57.720046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 20:49:57.720613 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.763 3.857 20.253
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 25.593 | 1.317 | 18.529 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.010 | 0.004 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.013 | |
| generate_dataset | 0.011 | 0.000 | 0.011 | |