Yannis Schumann
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 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 2024-06-28 17:41 -0400 (Fri, 28 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" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| 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 | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | 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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-26 23:15:17 -0400 (Wed, 26 Jun 2024) |
| EndedAt: 2024-06-26 23:17:33 -0400 (Wed, 26 Jun 2024) |
| EllapsedTime: 136.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.0.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.38 0.47 18.87
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2024-06-26 23:16:20.681207 INFO::Formatting Data.
2024-06-26 23:16:20.684188 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:20.698679 INFO::Removing potential empty rows and columns
2024-06-26 23:16:21.028427 INFO::Found 0 missing values.
2024-06-26 23:16:21.033424 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:21.03482 INFO::Done
2024-06-26 23:16:21.036051 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:21.056282 INFO::Starting hierarchical adjustment
2024-06-26 23:16:21.058001 INFO::Found 3 batches.
2024-06-26 23:16:21.059284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:21.061299 INFO::Using default BPPARAM
2024-06-26 23:16:21.062516 INFO::Processing subtree level 1
2024-06-26 23:16:23.933318 INFO::Adjusting the last 1 batches sequentially
2024-06-26 23:16:23.935527 INFO::Done
2024-06-26 23:16:23.936989 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:23.940447 INFO::ASW Batch was -0.128956243899805 prior to batch effect correction and is now -0.128956243899805 .
2024-06-26 23:16:23.942321 INFO::Total function execution time is 3.26170516014099 s and adjustment time is 2.87782096862793 s ( 88.23 )
2024-06-26 23:16:23.968734 INFO::Formatting Data.
2024-06-26 23:16:23.970203 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:23.971958 INFO::Removing potential empty rows and columns
2024-06-26 23:16:23.973979 INFO::Found 0 missing values.
2024-06-26 23:16:23.975708 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.
2024-06-26 23:16:23.990348 INFO::Formatting Data.
2024-06-26 23:16:23.991919 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:23.993783 INFO::Removing potential empty rows and columns
2024-06-26 23:16:23.995648 INFO::Found 0 missing values.
2024-06-26 23:16:23.997378 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.
2024-06-26 23:16:24.026651 INFO::Formatting Data.
2024-06-26 23:16:24.028472 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:24.030585 INFO::Removing potential empty rows and columns
2024-06-26 23:16:24.032649 INFO::Found 0 missing values.
2024-06-26 23:16:24.034431 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.
2024-06-26 23:16:24.040647 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:24.041916 INFO::Done
2024-06-26 23:16:24.043146 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:24.046527 INFO::Starting hierarchical adjustment
2024-06-26 23:16:24.048051 INFO::Found 2 batches.
2024-06-26 23:16:24.04938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:24.050716 INFO::Using default BPPARAM
2024-06-26 23:16:24.051948 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:24.053748 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:24.081104 INFO::Done
2024-06-26 23:16:24.082542 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:24.085972 INFO::ASW Batch was 0.0450201442413954 prior to batch effect correction and is now -0.115639504561284 .
2024-06-26 23:16:24.087553 INFO::Total function execution time is 0.0610189437866211 s and adjustment time is 0.0332069396972656 s ( 54.42 )
2024-06-26 23:16:24.091862 INFO::Formatting Data.
2024-06-26 23:16:24.093198 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:24.104962 INFO::Formatting Data.
2024-06-26 23:16:24.106473 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:24.10819 INFO::Removing potential empty rows and columns
2024-06-26 23:16:24.110075 INFO::Found 0 missing values.
2024-06-26 23:16:24.114508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:24.115842 INFO::Done
2024-06-26 23:16:24.117065 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:24.120505 INFO::Starting hierarchical adjustment
2024-06-26 23:16:24.121923 INFO::Found 2 batches.
2024-06-26 23:16:24.123139 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:24.124465 INFO::Using default BPPARAM
2024-06-26 23:16:24.125765 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:24.127731 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:24.148362 INFO::Done
2024-06-26 23:16:24.149815 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:24.15325 INFO::ASW Batch was 0.0086615216987662 prior to batch effect correction and is now -0.135314395741739 .
2024-06-26 23:16:24.154846 INFO::Total function execution time is 0.0500428676605225 s and adjustment time is 0.0266098976135254 s ( 53.17 )
2024-06-26 23:16:24.157232 INFO::Formatting Data.
2024-06-26 23:16:24.160845 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:24.162591 INFO::Removing potential empty rows and columns
2024-06-26 23:16:24.164467 INFO::Found 0 missing values.
2024-06-26 23:16:24.169503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:24.170819 INFO::Done
2024-06-26 23:16:24.172093 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:24.1756 INFO::Starting hierarchical adjustment
2024-06-26 23:16:24.17708 INFO::Found 2 batches.
2024-06-26 23:16:24.178299 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:24.179646 INFO::Using default BPPARAM
2024-06-26 23:16:24.180871 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:24.182671 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:24.203873 INFO::Done
2024-06-26 23:16:24.205549 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:24.209142 INFO::ASW Batch was 0.0086615216987662 prior to batch effect correction and is now -0.135314395741739 .
2024-06-26 23:16:24.210767 INFO::Total function execution time is 0.0535259246826172 s and adjustment time is 0.0269558429718018 s ( 50.36 )
2024-06-26 23:16:26.477151 INFO::Formatting Data.
2024-06-26 23:16:26.478193 INFO::Recognized SummarizedExperiment
2024-06-26 23:16:26.478947 INFO::Typecasting input to dataframe.
2024-06-26 23:16:26.514022 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:26.515509 INFO::Removing potential empty rows and columns
2024-06-26 23:16:26.518768 INFO::Found 0 missing values.
2024-06-26 23:16:27.343913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:27.344949 INFO::Done
2024-06-26 23:16:27.345732 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:27.34942 INFO::Starting hierarchical adjustment
2024-06-26 23:16:27.350336 INFO::Found 2 batches.
2024-06-26 23:16:27.351071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:27.352325 INFO::Using default BPPARAM
2024-06-26 23:16:27.353049 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:27.354223 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:27.400341 INFO::Done
2024-06-26 23:16:27.401368 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:27.405172 INFO::ASW Batch was -0.007170131122683 prior to batch effect correction and is now -0.0945884739868107 .
2024-06-26 23:16:27.406267 INFO::Total function execution time is 0.929532051086426 s and adjustment time is 0.0500988960266113 s ( 5.39 )
2024-06-26 23:16:27.425098 INFO::Formatting Data.
2024-06-26 23:16:27.42605 INFO::Recognized SummarizedExperiment
2024-06-26 23:16:27.42678 INFO::Typecasting input to dataframe.
2024-06-26 23:16:27.434532 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:27.435846 INFO::Removing potential empty rows and columns
2024-06-26 23:16:27.438748 INFO::Found 0 missing values.
2024-06-26 23:16:27.444076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:27.444946 INFO::Done
2024-06-26 23:16:27.445689 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:27.44955 INFO::Starting hierarchical adjustment
2024-06-26 23:16:27.450463 INFO::Found 2 batches.
2024-06-26 23:16:27.451176 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:27.451954 INFO::Using default BPPARAM
2024-06-26 23:16:27.452661 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:27.453914 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:27.473479 INFO::Done
2024-06-26 23:16:27.474398 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:27.478318 INFO::ASW Batch was 0.0114322118480563 prior to batch effect correction and is now 0.0114322118480563 .
2024-06-26 23:16:27.479383 INFO::Total function execution time is 0.0542562007904053 s and adjustment time is 0.0230951309204102 s ( 42.57 )
2024-06-26 23:16:27.500419 INFO::Formatting Data.
2024-06-26 23:16:27.501372 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:27.50246 INFO::Removing potential empty rows and columns
2024-06-26 23:16:27.503601 INFO::Found 0 missing values.
2024-06-26 23:16:27.506282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:27.507013 INFO::Done
2024-06-26 23:16:27.508006 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:27.511006 INFO::Starting hierarchical adjustment
2024-06-26 23:16:27.512333 INFO::Found 3 batches.
2024-06-26 23:16:27.513457 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:27.514647 INFO::Using default BPPARAM
2024-06-26 23:16:27.515693 INFO::Processing subtree level 1
2024-06-26 23:16:37.45415 INFO::Adjusting the last 1 batches sequentially
2024-06-26 23:16:37.456276 INFO::Done
2024-06-26 23:16:37.457582 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:37.460851 INFO::ASW Batch was -0.0681917241571501 prior to batch effect correction and is now -0.142853003713683 .
2024-06-26 23:16:37.462436 INFO::Total function execution time is 9.96203184127808 s and adjustment time is 9.94415497779846 s ( 99.82 )
2024-06-26 23:16:37.486874 INFO::Skipping initial DF formatting
2024-06-26 23:16:37.48831 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:37.49501 INFO::Starting hierarchical adjustment
2024-06-26 23:16:37.496631 INFO::Found 5 batches.
2024-06-26 23:16:37.497883 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:37.499212 INFO::Using default BPPARAM
2024-06-26 23:16:37.500363 INFO::Processing subtree level 1
2024-06-26 23:16:40.49356 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:40.495769 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:40.519857 INFO::Done
2024-06-26 23:16:40.52128 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:40.528213 INFO::ASW Batch was 0.52248792466013 prior to batch effect correction and is now 0.52248792466013 .
2024-06-26 23:16:40.529474 INFO::ASW Label was 0.332693172863104 prior to batch effect correction and is now 0.332693172863104 .
2024-06-26 23:16:40.53091 INFO::Total function execution time is 3.0441300868988 s and adjustment time is 3.02342414855957 s ( 99.32 )
2024-06-26 23:16:40.558086 INFO::Formatting Data.
2024-06-26 23:16:40.559064 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:40.56014 INFO::Removing potential empty rows and columns
2024-06-26 23:16:40.5613 INFO::Found 0 missing values.
2024-06-26 23:16:40.564855 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:40.5656 INFO::Done
2024-06-26 23:16:40.566395 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:40.569571 INFO::Starting hierarchical adjustment
2024-06-26 23:16:40.570475 INFO::Found 5 batches.
2024-06-26 23:16:40.57119 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:40.572019 INFO::Using default BPPARAM
2024-06-26 23:16:40.572737 INFO::Processing subtree level 1
2024-06-26 23:16:43.832754 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:43.834235 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:43.853189 INFO::Done
2024-06-26 23:16:43.854685 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:43.859529 INFO::ASW Batch was 0.613585511092418 prior to batch effect correction and is now -0.100659153866767 .
2024-06-26 23:16:43.861019 INFO::ASW Label was 0.176411639404516 prior to batch effect correction and is now 0.75757564937461 .
2024-06-26 23:16:43.86263 INFO::Total function execution time is 3.30457186698914 s and adjustment time is 3.28276109695435 s ( 99.34 )
2024-06-26 23:16:43.864304 INFO::Formatting Data.
2024-06-26 23:16:43.865682 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:43.867823 INFO::Removing potential empty rows and columns
2024-06-26 23:16:43.869955 INFO::Found 0 missing values.
2024-06-26 23:16:43.876214 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:43.877567 INFO::Done
2024-06-26 23:16:43.879222 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:43.88428 INFO::Starting hierarchical adjustment
2024-06-26 23:16:43.886185 INFO::Found 5 batches.
2024-06-26 23:16:43.88749 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:43.889156 INFO::Using default BPPARAM
2024-06-26 23:16:43.890421 INFO::Processing subtree level 1
2024-06-26 23:16:47.133517 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:47.135644 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:47.148778 INFO::Done
2024-06-26 23:16:47.149724 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:47.157859 INFO::ASW Batch was 0.613585511092418 prior to batch effect correction and is now -0.100659153866767 .
2024-06-26 23:16:47.158801 INFO::ASW Label was 0.176411639404516 prior to batch effect correction and is now 0.75757564937461 .
2024-06-26 23:16:47.159913 INFO::Total function execution time is 3.29569292068481 s and adjustment time is 3.26316404342651 s ( 99.01 )
2024-06-26 23:16:47.186198 INFO::Formatting Data.
2024-06-26 23:16:47.187866 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:47.189681 INFO::Removing potential empty rows and columns
2024-06-26 23:16:47.191821 INFO::Found 0 missing values.
2024-06-26 23:16:47.199263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:47.200824 INFO::Done
2024-06-26 23:16:47.20221 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:47.206861 INFO::Starting hierarchical adjustment
2024-06-26 23:16:47.208506 INFO::Found 5 batches.
2024-06-26 23:16:47.209765 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:47.211066 INFO::Using default BPPARAM
2024-06-26 23:16:47.212348 INFO::Processing subtree level 1
2024-06-26 23:16:50.236194 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:50.238294 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:50.256553 INFO::Done
2024-06-26 23:16:50.257936 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:50.262535 INFO::ASW Batch was 0.319003827414111 prior to batch effect correction and is now -0.103899363774528 .
2024-06-26 23:16:50.263809 INFO::ASW Label was 0.284950940549722 prior to batch effect correction and is now 0.853255583052962 .
2024-06-26 23:16:50.265343 INFO::Total function execution time is 3.07925915718079 s and adjustment time is 3.04826998710632 s ( 98.99 )
2024-06-26 23:16:50.26683 INFO::Formatting Data.
2024-06-26 23:16:50.268055 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:50.269493 INFO::Removing potential empty rows and columns
2024-06-26 23:16:50.270611 INFO::Found 0 missing values.
2024-06-26 23:16:50.27397 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:50.274688 INFO::Done
2024-06-26 23:16:50.275377 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:50.278252 INFO::Starting hierarchical adjustment
2024-06-26 23:16:50.279551 INFO::Found 5 batches.
2024-06-26 23:16:50.280622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:50.281798 INFO::Using default BPPARAM
2024-06-26 23:16:50.282527 INFO::Processing subtree level 1
2024-06-26 23:16:53.472407 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:53.474504 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:53.492841 INFO::Done
2024-06-26 23:16:53.494247 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:53.498924 INFO::ASW Batch was 0.319003827414111 prior to batch effect correction and is now -0.103899363774528 .
2024-06-26 23:16:53.500244 INFO::ASW Label was 0.284950940549722 prior to batch effect correction and is now 0.853255583052962 .
2024-06-26 23:16:53.501822 INFO::Total function execution time is 3.23498201370239 s and adjustment time is 3.21344208717346 s ( 99.33 )
2024-06-26 23:16:53.521148 INFO::Formatting Data.
2024-06-26 23:16:53.522677 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:53.52444 INFO::Removing potential empty rows and columns
2024-06-26 23:16:53.526299 INFO::Found 0 missing values.
2024-06-26 23:16:53.530403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:53.531633 INFO::Done
2024-06-26 23:16:53.532828 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:53.537463 INFO::Starting hierarchical adjustment
2024-06-26 23:16:53.538926 INFO::Found 2 batches.
2024-06-26 23:16:53.540117 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:53.541403 INFO::Using default BPPARAM
2024-06-26 23:16:53.542574 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:53.544311 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:53.565036 INFO::Done
2024-06-26 23:16:53.566386 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:53.571125 INFO::ASW Batch was 0.4160969652071 prior to batch effect correction and is now 0.0609125106299926 .
2024-06-26 23:16:53.572437 INFO::ASW Label was 0.661579173380844 prior to batch effect correction and is now 0.87306619489036 .
2024-06-26 23:16:53.573917 INFO::Total function execution time is 0.0528771877288818 s and adjustment time is 0.0262861251831055 s ( 49.71 )
2024-06-26 23:16:53.575348 INFO::Formatting Data.
2024-06-26 23:16:53.576562 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:53.57813 INFO::Removing potential empty rows and columns
2024-06-26 23:16:53.579801 INFO::Found 0 missing values.
2024-06-26 23:16:53.583782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:53.584935 INFO::Done
2024-06-26 23:16:53.586065 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:53.590709 INFO::Starting hierarchical adjustment
2024-06-26 23:16:53.592189 INFO::Found 2 batches.
2024-06-26 23:16:53.593361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:53.594618 INFO::Using default BPPARAM
2024-06-26 23:16:53.595774 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:53.597516 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:53.616707 INFO::Done
2024-06-26 23:16:53.61779 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:53.621136 INFO::ASW Batch was 0.4160969652071 prior to batch effect correction and is now 0.0609125106299926 .
2024-06-26 23:16:53.621986 INFO::ASW Label was 0.661579173380844 prior to batch effect correction and is now 0.87306619489036 .
2024-06-26 23:16:53.622985 INFO::Total function execution time is 0.0477259159088135 s and adjustment time is 0.0247161388397217 s ( 51.79 )
2024-06-26 23:16:53.639349 INFO::Formatting Data.
2024-06-26 23:16:53.640374 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:53.641477 INFO::Removing potential empty rows and columns
2024-06-26 23:16:53.642622 INFO::Found 0 missing values.
2024-06-26 23:16:53.644695 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:53.645428 INFO::Done
2024-06-26 23:16:53.646124 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:53.648131 INFO::Starting hierarchical adjustment
2024-06-26 23:16:53.649002 INFO::Found 2 batches.
2024-06-26 23:16:53.649737 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:53.650518 INFO::Using default BPPARAM
2024-06-26 23:16:53.651223 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:53.652291 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:53.677335 INFO::Done
2024-06-26 23:16:53.678236 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:53.680422 INFO::ASW Batch was -0.0899209384094614 prior to batch effect correction and is now -0.155412279675151 .
2024-06-26 23:16:53.681441 INFO::Total function execution time is 0.042186975479126 s and adjustment time is 0.0284221172332764 s ( 67.37 )
2024-06-26 23:16:53.697169 INFO::Formatting Data.
2024-06-26 23:16:53.698173 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:53.699355 INFO::Removing potential empty rows and columns
2024-06-26 23:16:53.700551 INFO::Found 0 missing values.
2024-06-26 23:16:53.701826 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.
2024-06-26 23:16:53.705764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:53.706558 INFO::Done
2024-06-26 23:16:53.707285 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:53.710261 INFO::Starting hierarchical adjustment
2024-06-26 23:16:53.711173 INFO::Found 2 batches.
2024-06-26 23:16:53.711916 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:53.712734 INFO::Using default BPPARAM
2024-06-26 23:16:53.713448 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:53.71452 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:53.728583 INFO::Done
2024-06-26 23:16:53.729504 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:53.73258 INFO::ASW Batch was 0.388854299712914 prior to batch effect correction and is now 0.0147290504456386 .
2024-06-26 23:16:53.733383 INFO::ASW Label was 0.668625598265049 prior to batch effect correction and is now 0.900207030066627 .
2024-06-26 23:16:53.734368 INFO::Total function execution time is 0.0373179912567139 s and adjustment time is 0.01751708984375 s ( 46.94 )
2024-06-26 23:16:53.735316 INFO::Formatting Data.
2024-06-26 23:16:53.736117 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:53.737181 INFO::Removing potential empty rows and columns
2024-06-26 23:16:53.73836 INFO::Found 0 missing values.
2024-06-26 23:16:53.739459 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.
2024-06-26 23:16:53.743651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:53.744421 INFO::Done
2024-06-26 23:16:53.745269 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:53.74873 INFO::Starting hierarchical adjustment
2024-06-26 23:16:53.74971 INFO::Found 2 batches.
2024-06-26 23:16:53.750499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:53.75136 INFO::Using default BPPARAM
2024-06-26 23:16:53.752145 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:16:53.753363 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:16:53.767358 INFO::Done
2024-06-26 23:16:53.768249 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:53.771376 INFO::ASW Batch was 0.388854299712914 prior to batch effect correction and is now 0.0147290504456386 .
2024-06-26 23:16:53.772183 INFO::ASW Label was 0.668625598265049 prior to batch effect correction and is now 0.900207030066627 .
2024-06-26 23:16:53.773189 INFO::Total function execution time is 0.0378689765930176 s and adjustment time is 0.0178008079528809 s ( 47.01 )
2024-06-26 23:16:54.025369 INFO::Formatting Data.
2024-06-26 23:16:54.027073 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:54.029435 INFO::Removing potential empty rows and columns
2024-06-26 23:16:54.032089 INFO::Found 0 missing values.
2024-06-26 23:16:54.038201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:54.03969 INFO::Done
2024-06-26 23:16:54.041071 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:54.044999 INFO::Starting hierarchical adjustment
2024-06-26 23:16:54.04662 INFO::Found 3 batches.
2024-06-26 23:16:54.047973 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:54.049404 INFO::Using default BPPARAM
2024-06-26 23:16:54.050678 INFO::Processing subtree level 1
2024-06-26 23:16:56.919128 INFO::Adjusting the last 1 batches sequentially
2024-06-26 23:16:56.92074 INFO::Done
2024-06-26 23:16:56.922024 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:56.925303 INFO::ASW Batch was -0.106915851054901 prior to batch effect correction and is now -0.106915851054901 .
2024-06-26 23:16:56.926888 INFO::Total function execution time is 2.90166592597961 s and adjustment time is 2.87439918518066 s ( 99.06 )
2024-06-26 23:16:56.928689 INFO::Formatting Data.
2024-06-26 23:16:56.930013 INFO::Typecasting input to dataframe.
2024-06-26 23:16:56.931491 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:56.93313 INFO::Removing potential empty rows and columns
2024-06-26 23:16:56.934873 INFO::Found 0 missing values.
2024-06-26 23:16:56.939231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:56.940415 INFO::Done
2024-06-26 23:16:56.941581 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:56.944706 INFO::Starting hierarchical adjustment
2024-06-26 23:16:56.946064 INFO::Found 3 batches.
2024-06-26 23:16:56.947201 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:56.948443 INFO::Using default BPPARAM
2024-06-26 23:16:56.949574 INFO::Processing subtree level 1
2024-06-26 23:16:59.57981 INFO::Adjusting the last 1 batches sequentially
2024-06-26 23:16:59.58198 INFO::Done
2024-06-26 23:16:59.583219 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:16:59.586163 INFO::ASW Batch was -0.106915851054901 prior to batch effect correction and is now -0.106915851054901 .
2024-06-26 23:16:59.587622 INFO::Total function execution time is 2.65896892547607 s and adjustment time is 2.63609290122986 s ( 99.14 )
2024-06-26 23:16:59.607311 INFO::Formatting Data.
2024-06-26 23:16:59.608336 INFO::Typecasting input to dataframe.
2024-06-26 23:16:59.609398 INFO::Replacing NaNs with NAs.
2024-06-26 23:16:59.610462 INFO::Removing potential empty rows and columns
2024-06-26 23:16:59.611622 INFO::Found 0 missing values.
2024-06-26 23:16:59.614317 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:16:59.615043 INFO::Done
2024-06-26 23:16:59.615773 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:16:59.617839 INFO::Starting hierarchical adjustment
2024-06-26 23:16:59.618702 INFO::Found 3 batches.
2024-06-26 23:16:59.619446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:16:59.620254 INFO::Using default BPPARAM
2024-06-26 23:16:59.620965 INFO::Processing subtree level 1
2024-06-26 23:17:02.325726 INFO::Adjusting the last 1 batches sequentially
2024-06-26 23:17:02.327211 INFO::Done
2024-06-26 23:17:02.327985 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:17:02.330263 INFO::ASW Batch was 0.0242388257266673 prior to batch effect correction and is now 0.0242388257266673 .
2024-06-26 23:17:02.331231 INFO::Total function execution time is 2.72404885292053 s and adjustment time is 2.70862984657288 s ( 99.43 )
2024-06-26 23:17:05.174214 INFO::Formatting Data.
2024-06-26 23:17:05.175212 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:05.176421 INFO::Removing potential empty rows and columns
2024-06-26 23:17:05.178654 INFO::Found 1000 missing values.
2024-06-26 23:17:05.191885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:05.192814 INFO::Done
2024-06-26 23:17:05.19356 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:17:05.199605 INFO::Starting hierarchical adjustment
2024-06-26 23:17:05.2006 INFO::Found 10 batches.
2024-06-26 23:17:05.201331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:17:05.202099 INFO::Using default BPPARAM
2024-06-26 23:17:05.202802 INFO::Processing subtree level 1
2024-06-26 23:17:08.794209 INFO::Processing subtree level 2
2024-06-26 23:17:11.634127 INFO::Adjusting the last 1 batches sequentially
2024-06-26 23:17:11.63573 INFO::Done
2024-06-26 23:17:11.636706 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:17:11.642952 INFO::ASW Batch was 0.496931351184438 prior to batch effect correction and is now 0.496931351184438 .
2024-06-26 23:17:11.64386 INFO::ASW Label was 0.322717600751875 prior to batch effect correction and is now 0.322717600751875 .
2024-06-26 23:17:11.644941 INFO::Total function execution time is 6.47080779075623 s and adjustment time is 6.43527317047119 s ( 99.45 )
2024-06-26 23:17:11.645968 INFO::Formatting Data.
2024-06-26 23:17:11.646838 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:11.648054 INFO::Removing potential empty rows and columns
2024-06-26 23:17:11.650252 INFO::Found 1000 missing values.
2024-06-26 23:17:11.663928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:11.664922 INFO::Done
2024-06-26 23:17:11.665866 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:17:11.676935 INFO::Starting hierarchical adjustment
2024-06-26 23:17:11.678108 INFO::Found 10 batches.
2024-06-26 23:17:12.433883 INFO::Set up parallel execution backend with 2 workers
2024-06-26 23:17:12.434848 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-26 23:17:15.390594 INFO::Adjusting the last 2 batches sequentially
2024-06-26 23:17:15.392726 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-26 23:17:15.416481 INFO::Done
2024-06-26 23:17:15.417838 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:17:15.426367 INFO::ASW Batch was 0.496931351184438 prior to batch effect correction and is now 0.496931351184438 .
2024-06-26 23:17:15.427296 INFO::ASW Label was 0.322717600751875 prior to batch effect correction and is now 0.322717600751875 .
2024-06-26 23:17:15.428336 INFO::Total function execution time is 3.78236103057861 s and adjustment time is 3.73846292495728 s ( 98.84 )
2024-06-26 23:17:18.825627 INFO::Formatting Data.
2024-06-26 23:17:18.827139 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:18.828872 INFO::Removing potential empty rows and columns
2024-06-26 23:17:18.830731 INFO::Found 0 missing values.
2024-06-26 23:17:18.836101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:18.837426 INFO::Done
2024-06-26 23:17:18.838687 INFO::Acquiring quality metrics before batch effect correction.
2024-06-26 23:17:18.84311 INFO::Starting hierarchical adjustment
2024-06-26 23:17:18.844676 INFO::Found 3 batches.
2024-06-26 23:17:18.845942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-26 23:17:18.847263 INFO::Using default BPPARAM
2024-06-26 23:17:18.848483 INFO::Processing subtree level 1
2024-06-26 23:17:22.285464 INFO::Adjusting the last 1 batches sequentially
2024-06-26 23:17:22.287599 INFO::Done
2024-06-26 23:17:22.288884 INFO::Acquiring quality metrics after batch effect correction.
2024-06-26 23:17:22.295722 INFO::ASW Batch was 0.240921837848399 prior to batch effect correction and is now -0.141480677108445 .
2024-06-26 23:17:22.297191 INFO::ASW Label was -0.199568797411613 prior to batch effect correction and is now -0.0444552560751696 .
2024-06-26 23:17:22.298875 INFO::Total function execution time is 3.47328209877014 s and adjustment time is 3.44315314292908 s ( 99.13 )
2024-06-26 23:17:22.520962 INFO::Formatting Data.
2024-06-26 23:17:22.522553 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.524298 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.526194 INFO::Found 2 missing values.
2024-06-26 23:17:22.529076 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.529918 INFO::Done
2024-06-26 23:17:22.591886 INFO::Found NA in Reference column
2024-06-26 23:17:22.611755 INFO::Require at least two references per batch.
2024-06-26 23:17:22.645384 INFO::Formatting Data.
2024-06-26 23:17:22.647129 INFO::Recognized SummarizedExperiment
2024-06-26 23:17:22.648426 INFO::Typecasting input to dataframe.
2024-06-26 23:17:22.658834 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.660175 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.663045 INFO::Found 0 missing values.
2024-06-26 23:17:22.669102 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.670303 INFO::Done
2024-06-26 23:17:22.690409 INFO::Formatting Data.
2024-06-26 23:17:22.69193 INFO::Recognized SummarizedExperiment
2024-06-26 23:17:22.693238 INFO::Typecasting input to dataframe.
2024-06-26 23:17:22.715711 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.717263 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.720499 INFO::Found 0 missing values.
2024-06-26 23:17:22.733216 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.734709 INFO::Done
2024-06-26 23:17:22.755009 INFO::Formatting Data.
2024-06-26 23:17:22.756064 INFO::Recognized SummarizedExperiment
2024-06-26 23:17:22.757016 INFO::Typecasting input to dataframe.
2024-06-26 23:17:22.780639 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.782586 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.784723 INFO::Found 0 missing values.
2024-06-26 23:17:22.786658 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.
2024-06-26 23:17:22.793469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.794879 INFO::Done
2024-06-26 23:17:22.816952 INFO::Formatting Data.
2024-06-26 23:17:22.818516 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.82049 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.822399 INFO::Found 0 missing values.
2024-06-26 23:17:22.825979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.826741 INFO::Done
2024-06-26 23:17:22.843372 INFO::Formatting Data.
2024-06-26 23:17:22.844363 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.845433 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.846572 INFO::Found 0 missing values.
2024-06-26 23:17:22.849268 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.849991 INFO::Done
2024-06-26 23:17:22.902474 INFO::Formatting Data.
2024-06-26 23:17:22.903504 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.904711 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.906048 INFO::Found 1 missing values.
2024-06-26 23:17:22.908421 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.909163 INFO::Done
2024-06-26 23:17:22.936168 INFO::Formatting Data.
2024-06-26 23:17:22.937216 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.93831 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.939466 INFO::Found 2 missing values.
2024-06-26 23:17:22.940548 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.
2024-06-26 23:17:22.94275 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.943484 INFO::Done
2024-06-26 23:17:22.958284 INFO::Formatting Data.
2024-06-26 23:17:22.959278 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.960328 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.961512 INFO::Found 2 missing values.
2024-06-26 23:17:22.963282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.964097 INFO::Done
2024-06-26 23:17:22.979861 INFO::Formatting Data.
2024-06-26 23:17:22.980893 INFO::Typecasting input to dataframe.
2024-06-26 23:17:22.982109 INFO::Replacing NaNs with NAs.
2024-06-26 23:17:22.983199 INFO::Removing potential empty rows and columns
2024-06-26 23:17:22.984318 INFO::Found 0 missing values.
2024-06-26 23:17:22.98696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-26 23:17:22.98769 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.68 1.51 77.34
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.38 | 0.47 | 18.87 | |
| compute_asw | 0.04 | 0.00 | 0.05 | |
| count_existing | 0.03 | 0.00 | 0.03 | |
| generate_data_covariables | 0.02 | 0.00 | 0.01 | |
| generate_dataset | 0.02 | 0.01 | 0.03 | |