Yannis Schumann
| Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-15 11:39 -0400 (Mon, 15 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 154/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | 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: 1.1.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-07-14 21:35:04 -0400 (Sun, 14 Jul 2024) |
| EndedAt: 2024-07-14 21:36:59 -0400 (Sun, 14 Jul 2024) |
| EllapsedTime: 115.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '1.1.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 6.62 4.11 17.31
* 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: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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")
2024-07-14 21:35:59.997654 INFO::Formatting Data.
2024-07-14 21:36:00.000231 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:00.009027 INFO::Removing potential empty rows and columns
2024-07-14 21:36:00.208507 INFO::Found 0 missing values.
2024-07-14 21:36:00.211803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:00.212591 INFO::Done
2024-07-14 21:36:00.213276 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:00.226929 INFO::Starting hierarchical adjustment
2024-07-14 21:36:00.227838 INFO::Found 3 batches.
2024-07-14 21:36:00.228486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:00.229722 INFO::Using default BPPARAM
2024-07-14 21:36:00.230447 INFO::Processing subtree level 1
2024-07-14 21:36:02.831365 INFO::Adjusting the last 1 batches sequentially
2024-07-14 21:36:02.832989 INFO::Done
2024-07-14 21:36:02.833835 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:02.83594 INFO::ASW Batch was -0.0657951442069827 prior to batch effect correction and is now -0.0657951442069827 .
2024-07-14 21:36:02.836999 INFO::Total function execution time is 2.83989691734314 s and adjustment time is 2.60526585578918 s ( 91.74 )
2024-07-14 21:36:02.857283 INFO::Formatting Data.
2024-07-14 21:36:02.858158 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:02.859103 INFO::Removing potential empty rows and columns
2024-07-14 21:36:02.860123 INFO::Found 0 missing values.
2024-07-14 21:36:02.861052 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-14 21:36:02.868197 INFO::Formatting Data.
2024-07-14 21:36:02.868914 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:02.869803 INFO::Removing potential empty rows and columns
2024-07-14 21:36:02.870783 INFO::Found 0 missing values.
2024-07-14 21:36:02.871668 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-14 21:36:02.889061 INFO::Formatting Data.
2024-07-14 21:36:02.890413 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:02.891832 INFO::Removing potential empty rows and columns
2024-07-14 21:36:02.893303 INFO::Found 0 missing values.
2024-07-14 21:36:02.894542 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-14 21:36:02.898549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:02.899334 INFO::Done
2024-07-14 21:36:02.900114 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:02.90232 INFO::Starting hierarchical adjustment
2024-07-14 21:36:02.903295 INFO::Found 2 batches.
2024-07-14 21:36:02.9238 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:02.924791 INFO::Using default BPPARAM
2024-07-14 21:36:02.925589 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:02.926591 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:02.942238 INFO::Done
2024-07-14 21:36:02.942945 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:02.944902 INFO::ASW Batch was 0.0411930249196863 prior to batch effect correction and is now -0.117400541305978 .
2024-07-14 21:36:02.945825 INFO::Total function execution time is 0.0569608211517334 s and adjustment time is 0.0391979217529297 s ( 68.82 )
2024-07-14 21:36:02.948539 INFO::Formatting Data.
2024-07-14 21:36:02.949272 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:02.95595 INFO::Formatting Data.
2024-07-14 21:36:02.956685 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:02.957587 INFO::Removing potential empty rows and columns
2024-07-14 21:36:02.958644 INFO::Found 0 missing values.
2024-07-14 21:36:02.96091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:02.961615 INFO::Done
2024-07-14 21:36:02.962233 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:02.964071 INFO::Starting hierarchical adjustment
2024-07-14 21:36:02.964861 INFO::Found 2 batches.
2024-07-14 21:36:02.965478 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:02.966157 INFO::Using default BPPARAM
2024-07-14 21:36:02.96676 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:02.967656 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:02.978884 INFO::Done
2024-07-14 21:36:02.97955 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:02.981419 INFO::ASW Batch was 0.0316226718301263 prior to batch effect correction and is now -0.115088190976616 .
2024-07-14 21:36:02.982264 INFO::Total function execution time is 0.0263040065765381 s and adjustment time is 0.0141539573669434 s ( 53.81 )
2024-07-14 21:36:02.983319 INFO::Formatting Data.
2024-07-14 21:36:02.98403 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:02.98495 INFO::Removing potential empty rows and columns
2024-07-14 21:36:02.985952 INFO::Found 0 missing values.
2024-07-14 21:36:02.988326 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:02.989033 INFO::Done
2024-07-14 21:36:02.989689 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:02.991477 INFO::Starting hierarchical adjustment
2024-07-14 21:36:02.992312 INFO::Found 2 batches.
2024-07-14 21:36:02.992958 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:02.99364 INFO::Using default BPPARAM
2024-07-14 21:36:02.994251 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:02.995142 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:03.006516 INFO::Done
2024-07-14 21:36:03.007207 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:03.009113 INFO::ASW Batch was 0.0316226718301263 prior to batch effect correction and is now -0.115088190976616 .
2024-07-14 21:36:03.010003 INFO::Total function execution time is 0.0266640186309814 s and adjustment time is 0.0143270492553711 s ( 53.73 )
2024-07-14 21:36:05.229393 INFO::Formatting Data.
2024-07-14 21:36:05.230265 INFO::Recognized SummarizedExperiment
2024-07-14 21:36:05.230902 INFO::Typecasting input to dataframe.
2024-07-14 21:36:05.255575 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:05.256806 INFO::Removing potential empty rows and columns
2024-07-14 21:36:05.25961 INFO::Found 0 missing values.
2024-07-14 21:36:05.264616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:05.265398 INFO::Done
2024-07-14 21:36:05.266061 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:05.269619 INFO::Starting hierarchical adjustment
2024-07-14 21:36:05.270427 INFO::Found 2 batches.
2024-07-14 21:36:05.271054 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:05.272106 INFO::Using default BPPARAM
2024-07-14 21:36:05.272743 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:05.273806 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:05.315861 INFO::Done
2024-07-14 21:36:05.316805 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:05.320608 INFO::ASW Batch was 0.00818897733387016 prior to batch effect correction and is now -0.091286719452583 .
2024-07-14 21:36:05.321705 INFO::Total function execution time is 0.0925321578979492 s and adjustment time is 0.0455079078674316 s ( 49.18 )
2024-07-14 21:36:05.339588 INFO::Formatting Data.
2024-07-14 21:36:05.34041 INFO::Recognized SummarizedExperiment
2024-07-14 21:36:05.341137 INFO::Typecasting input to dataframe.
2024-07-14 21:36:05.350072 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:05.35139 INFO::Removing potential empty rows and columns
2024-07-14 21:36:05.355049 INFO::Found 0 missing values.
2024-07-14 21:36:05.361688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:05.362439 INFO::Done
2024-07-14 21:36:05.363214 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:05.367408 INFO::Starting hierarchical adjustment
2024-07-14 21:36:05.36834 INFO::Found 2 batches.
2024-07-14 21:36:05.369083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:05.369913 INFO::Using default BPPARAM
2024-07-14 21:36:05.370657 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:05.371847 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:05.395646 INFO::Done
2024-07-14 21:36:05.396611 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:05.400739 INFO::ASW Batch was 0.0270781472577091 prior to batch effect correction and is now 0.0270781472577091 .
2024-07-14 21:36:05.401826 INFO::Total function execution time is 0.0622129440307617 s and adjustment time is 0.0274050235748291 s ( 44.05 )
2024-07-14 21:36:05.424126 INFO::Formatting Data.
2024-07-14 21:36:05.425129 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:05.426295 INFO::Removing potential empty rows and columns
2024-07-14 21:36:05.427534 INFO::Found 0 missing values.
2024-07-14 21:36:05.430464 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:05.43121 INFO::Done
2024-07-14 21:36:05.431906 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:05.434141 INFO::Starting hierarchical adjustment
2024-07-14 21:36:05.435031 INFO::Found 3 batches.
2024-07-14 21:36:05.435734 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:05.436553 INFO::Using default BPPARAM
2024-07-14 21:36:05.437281 INFO::Processing subtree level 1
2024-07-14 21:36:13.538786 INFO::Adjusting the last 1 batches sequentially
2024-07-14 21:36:13.54038 INFO::Done
2024-07-14 21:36:13.541214 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:13.543298 INFO::ASW Batch was 0.00971005356583009 prior to batch effect correction and is now -0.191294737647988 .
2024-07-14 21:36:13.54424 INFO::Total function execution time is 8.12021899223328 s and adjustment time is 8.10545802116394 s ( 99.82 )
2024-07-14 21:36:13.561299 INFO::Skipping initial DF formatting
2024-07-14 21:36:13.562127 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:13.566014 INFO::Starting hierarchical adjustment
2024-07-14 21:36:13.56688 INFO::Found 5 batches.
2024-07-14 21:36:13.567509 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:13.568191 INFO::Using default BPPARAM
2024-07-14 21:36:13.56882 INFO::Processing subtree level 1
2024-07-14 21:36:16.32844 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:16.329904 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:16.343803 INFO::Done
2024-07-14 21:36:16.344572 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:16.348653 INFO::ASW Batch was 0.532005934456421 prior to batch effect correction and is now 0.532005934456421 .
2024-07-14 21:36:16.349377 INFO::ASW Label was 0.329024215842487 prior to batch effect correction and is now 0.329024215842487 .
2024-07-14 21:36:16.350251 INFO::Total function execution time is 2.78907799720764 s and adjustment time is 2.77700591087341 s ( 99.57 )
2024-07-14 21:36:16.368209 INFO::Formatting Data.
2024-07-14 21:36:16.368945 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:16.369826 INFO::Removing potential empty rows and columns
2024-07-14 21:36:16.370802 INFO::Found 0 missing values.
2024-07-14 21:36:16.373803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:16.374432 INFO::Done
2024-07-14 21:36:16.37508 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:16.377781 INFO::Starting hierarchical adjustment
2024-07-14 21:36:16.378564 INFO::Found 5 batches.
2024-07-14 21:36:16.379181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:16.379857 INFO::Using default BPPARAM
2024-07-14 21:36:16.380458 INFO::Processing subtree level 1
2024-07-14 21:36:18.808353 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:18.80995 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:18.821427 INFO::Done
2024-07-14 21:36:18.822182 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:18.825152 INFO::ASW Batch was 0.40861310358927 prior to batch effect correction and is now 0.0285918541590052 .
2024-07-14 21:36:18.825865 INFO::ASW Label was 0.407408464191993 prior to batch effect correction and is now 0.715923967219758 .
2024-07-14 21:36:18.826742 INFO::Total function execution time is 2.45855402946472 s and adjustment time is 2.44295287132263 s ( 99.37 )
2024-07-14 21:36:18.8276 INFO::Formatting Data.
2024-07-14 21:36:18.828482 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:18.829398 INFO::Removing potential empty rows and columns
2024-07-14 21:36:18.830356 INFO::Found 0 missing values.
2024-07-14 21:36:18.83336 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:18.833986 INFO::Done
2024-07-14 21:36:18.834603 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:18.837321 INFO::Starting hierarchical adjustment
2024-07-14 21:36:18.838092 INFO::Found 5 batches.
2024-07-14 21:36:18.8387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:18.839367 INFO::Using default BPPARAM
2024-07-14 21:36:18.839988 INFO::Processing subtree level 1
2024-07-14 21:36:21.239766 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:21.241311 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:21.252841 INFO::Done
2024-07-14 21:36:21.253613 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:21.256501 INFO::ASW Batch was 0.40861310358927 prior to batch effect correction and is now 0.0285918541590052 .
2024-07-14 21:36:21.257211 INFO::ASW Label was 0.407408464191993 prior to batch effect correction and is now 0.715923967219758 .
2024-07-14 21:36:21.258061 INFO::Total function execution time is 2.43047094345093 s and adjustment time is 2.41481995582581 s ( 99.36 )
2024-07-14 21:36:21.273277 INFO::Formatting Data.
2024-07-14 21:36:21.274132 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:21.275037 INFO::Removing potential empty rows and columns
2024-07-14 21:36:21.27599 INFO::Found 0 missing values.
2024-07-14 21:36:21.278958 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:21.279591 INFO::Done
2024-07-14 21:36:21.280198 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:21.282946 INFO::Starting hierarchical adjustment
2024-07-14 21:36:21.283844 INFO::Found 5 batches.
2024-07-14 21:36:21.284459 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:21.285163 INFO::Using default BPPARAM
2024-07-14 21:36:21.28577 INFO::Processing subtree level 1
2024-07-14 21:36:23.932629 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:23.934265 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:23.946453 INFO::Done
2024-07-14 21:36:23.94736 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:23.950686 INFO::ASW Batch was 0.380385009763932 prior to batch effect correction and is now -0.0256194796538284 .
2024-07-14 21:36:23.951464 INFO::ASW Label was 0.42370791246 prior to batch effect correction and is now 0.823611231027269 .
2024-07-14 21:36:23.952376 INFO::Total function execution time is 2.67910289764404 s and adjustment time is 2.66276502609253 s ( 99.39 )
2024-07-14 21:36:23.953286 INFO::Formatting Data.
2024-07-14 21:36:23.954014 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:23.955014 INFO::Removing potential empty rows and columns
2024-07-14 21:36:23.956008 INFO::Found 0 missing values.
2024-07-14 21:36:23.959146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:23.959859 INFO::Done
2024-07-14 21:36:23.960517 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:23.963491 INFO::Starting hierarchical adjustment
2024-07-14 21:36:23.964307 INFO::Found 5 batches.
2024-07-14 21:36:23.964954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:23.965653 INFO::Using default BPPARAM
2024-07-14 21:36:23.966277 INFO::Processing subtree level 1
2024-07-14 21:36:26.413023 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:26.41483 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:26.428179 INFO::Done
2024-07-14 21:36:26.429113 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:26.432328 INFO::ASW Batch was 0.380385009763932 prior to batch effect correction and is now -0.0256194796538284 .
2024-07-14 21:36:26.433153 INFO::ASW Label was 0.42370791246 prior to batch effect correction and is now 0.823611231027269 .
2024-07-14 21:36:26.434066 INFO::Total function execution time is 2.48076200485229 s and adjustment time is 2.46391987800598 s ( 99.32 )
2024-07-14 21:36:26.450262 INFO::Formatting Data.
2024-07-14 21:36:26.451205 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:26.452117 INFO::Removing potential empty rows and columns
2024-07-14 21:36:26.453115 INFO::Found 0 missing values.
2024-07-14 21:36:26.455203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:26.455827 INFO::Done
2024-07-14 21:36:26.456419 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:26.459323 INFO::Starting hierarchical adjustment
2024-07-14 21:36:26.460097 INFO::Found 2 batches.
2024-07-14 21:36:26.460706 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:26.461427 INFO::Using default BPPARAM
2024-07-14 21:36:26.462038 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:26.462959 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:26.473383 INFO::Done
2024-07-14 21:36:26.474033 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:26.476531 INFO::ASW Batch was 0.564882924115441 prior to batch effect correction and is now -0.0222666599637741 .
2024-07-14 21:36:26.477209 INFO::ASW Label was 0.456312722821667 prior to batch effect correction and is now 0.9300873215059 .
2024-07-14 21:36:26.477999 INFO::Total function execution time is 0.0278830528259277 s and adjustment time is 0.0134000778198242 s ( 48.06 )
2024-07-14 21:36:26.478923 INFO::Formatting Data.
2024-07-14 21:36:26.479589 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:26.480421 INFO::Removing potential empty rows and columns
2024-07-14 21:36:26.481359 INFO::Found 0 missing values.
2024-07-14 21:36:26.483383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:26.484007 INFO::Done
2024-07-14 21:36:26.484658 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:26.487188 INFO::Starting hierarchical adjustment
2024-07-14 21:36:26.487962 INFO::Found 2 batches.
2024-07-14 21:36:26.4886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:26.489302 INFO::Using default BPPARAM
2024-07-14 21:36:26.489906 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:26.490764 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:26.500816 INFO::Done
2024-07-14 21:36:26.501471 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:26.504046 INFO::ASW Batch was 0.564882924115441 prior to batch effect correction and is now -0.0222666599637741 .
2024-07-14 21:36:26.504709 INFO::ASW Label was 0.456312722821667 prior to batch effect correction and is now 0.9300873215059 .
2024-07-14 21:36:26.50552 INFO::Total function execution time is 0.0265810489654541 s and adjustment time is 0.0129501819610596 s ( 48.72 )
2024-07-14 21:36:26.520017 INFO::Formatting Data.
2024-07-14 21:36:26.520749 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:26.521619 INFO::Removing potential empty rows and columns
2024-07-14 21:36:26.522501 INFO::Found 0 missing values.
2024-07-14 21:36:26.524192 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:26.524848 INFO::Done
2024-07-14 21:36:26.525606 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:26.5272 INFO::Starting hierarchical adjustment
2024-07-14 21:36:26.528 INFO::Found 2 batches.
2024-07-14 21:36:26.528628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:26.529325 INFO::Using default BPPARAM
2024-07-14 21:36:26.529927 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:26.530795 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:26.552314 INFO::Done
2024-07-14 21:36:26.553031 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:26.554656 INFO::ASW Batch was -0.0461795203275004 prior to batch effect correction and is now -0.187418565153907 .
2024-07-14 21:36:26.555494 INFO::Total function execution time is 0.0354719161987305 s and adjustment time is 0.0244550704956055 s ( 68.94 )
2024-07-14 21:36:26.576888 INFO::Formatting Data.
2024-07-14 21:36:26.577978 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:26.578945 INFO::Removing potential empty rows and columns
2024-07-14 21:36:26.580162 INFO::Found 0 missing values.
2024-07-14 21:36:26.581351 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-14 21:36:26.584847 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:26.585485 INFO::Done
2024-07-14 21:36:26.586098 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:26.589087 INFO::Starting hierarchical adjustment
2024-07-14 21:36:26.589883 INFO::Found 2 batches.
2024-07-14 21:36:26.590513 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:26.591194 INFO::Using default BPPARAM
2024-07-14 21:36:26.591792 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:26.592683 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:26.604775 INFO::Done
2024-07-14 21:36:26.605472 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:26.608399 INFO::ASW Batch was 0.532862966312012 prior to batch effect correction and is now 0.00600528093413693 .
2024-07-14 21:36:26.609835 INFO::ASW Label was 0.54304663791879 prior to batch effect correction and is now 0.903694009776603 .
2024-07-14 21:36:26.610974 INFO::Total function execution time is 0.0346508026123047 s and adjustment time is 0.0150110721588135 s ( 43.32 )
2024-07-14 21:36:26.612163 INFO::Formatting Data.
2024-07-14 21:36:26.613052 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:26.613996 INFO::Removing potential empty rows and columns
2024-07-14 21:36:26.614953 INFO::Found 0 missing values.
2024-07-14 21:36:26.615918 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-14 21:36:26.619467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:26.620174 INFO::Done
2024-07-14 21:36:26.62094 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:26.623632 INFO::Starting hierarchical adjustment
2024-07-14 21:36:26.624411 INFO::Found 2 batches.
2024-07-14 21:36:26.625055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:26.625731 INFO::Using default BPPARAM
2024-07-14 21:36:26.626336 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:26.627221 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:26.639528 INFO::Done
2024-07-14 21:36:26.640195 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:26.642786 INFO::ASW Batch was 0.532862966312012 prior to batch effect correction and is now 0.00600528093413693 .
2024-07-14 21:36:26.643452 INFO::ASW Label was 0.54304663791879 prior to batch effect correction and is now 0.903694009776603 .
2024-07-14 21:36:26.644272 INFO::Total function execution time is 0.0321519374847412 s and adjustment time is 0.0152261257171631 s ( 47.36 )
2024-07-14 21:36:26.807155 INFO::Formatting Data.
2024-07-14 21:36:26.80819 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:26.809298 INFO::Removing potential empty rows and columns
2024-07-14 21:36:26.81052 INFO::Found 0 missing values.
2024-07-14 21:36:26.813311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:26.814005 INFO::Done
2024-07-14 21:36:26.814703 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:26.816887 INFO::Starting hierarchical adjustment
2024-07-14 21:36:26.817846 INFO::Found 3 batches.
2024-07-14 21:36:26.818557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:26.819318 INFO::Using default BPPARAM
2024-07-14 21:36:26.820015 INFO::Processing subtree level 1
2024-07-14 21:36:29.13917 INFO::Adjusting the last 1 batches sequentially
2024-07-14 21:36:29.140785 INFO::Done
2024-07-14 21:36:29.141668 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:29.143823 INFO::ASW Batch was -0.103103291578447 prior to batch effect correction and is now -0.103103291578447 .
2024-07-14 21:36:29.144783 INFO::Total function execution time is 2.33776593208313 s and adjustment time is 2.32311987876892 s ( 99.37 )
2024-07-14 21:36:29.146169 INFO::Formatting Data.
2024-07-14 21:36:29.14731 INFO::Typecasting input to dataframe.
2024-07-14 21:36:29.148348 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:29.149608 INFO::Removing potential empty rows and columns
2024-07-14 21:36:29.15121 INFO::Found 0 missing values.
2024-07-14 21:36:29.155407 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:29.156394 INFO::Done
2024-07-14 21:36:29.15734 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:29.160312 INFO::Starting hierarchical adjustment
2024-07-14 21:36:29.161485 INFO::Found 3 batches.
2024-07-14 21:36:29.162454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:29.163486 INFO::Using default BPPARAM
2024-07-14 21:36:29.164386 INFO::Processing subtree level 1
2024-07-14 21:36:32.033396 INFO::Adjusting the last 1 batches sequentially
2024-07-14 21:36:32.034844 INFO::Done
2024-07-14 21:36:32.035543 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:32.037395 INFO::ASW Batch was -0.103103291578447 prior to batch effect correction and is now -0.103103291578447 .
2024-07-14 21:36:32.038297 INFO::Total function execution time is 2.89235997200012 s and adjustment time is 2.87356090545654 s ( 99.35 )
2024-07-14 21:36:32.057022 INFO::Formatting Data.
2024-07-14 21:36:32.057988 INFO::Typecasting input to dataframe.
2024-07-14 21:36:32.058882 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:32.059817 INFO::Removing potential empty rows and columns
2024-07-14 21:36:32.060839 INFO::Found 0 missing values.
2024-07-14 21:36:32.063031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:32.063695 INFO::Done
2024-07-14 21:36:32.0643 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:32.066161 INFO::Starting hierarchical adjustment
2024-07-14 21:36:32.066929 INFO::Found 3 batches.
2024-07-14 21:36:32.067537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:32.068208 INFO::Using default BPPARAM
2024-07-14 21:36:32.068815 INFO::Processing subtree level 1
2024-07-14 21:36:34.349705 INFO::Adjusting the last 1 batches sequentially
2024-07-14 21:36:34.352022 INFO::Done
2024-07-14 21:36:34.353116 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:34.355837 INFO::ASW Batch was -0.0736876383080504 prior to batch effect correction and is now -0.0736876383080504 .
2024-07-14 21:36:34.357062 INFO::Total function execution time is 2.3002028465271 s and adjustment time is 2.28513598442078 s ( 99.34 )
2024-07-14 21:36:37.087071 INFO::Formatting Data.
2024-07-14 21:36:37.088041 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:37.089121 INFO::Removing potential empty rows and columns
2024-07-14 21:36:37.091345 INFO::Found 1000 missing values.
2024-07-14 21:36:37.104114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:37.104843 INFO::Done
2024-07-14 21:36:37.105513 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:37.111267 INFO::Starting hierarchical adjustment
2024-07-14 21:36:37.112075 INFO::Found 10 batches.
2024-07-14 21:36:37.112695 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:37.113409 INFO::Using default BPPARAM
2024-07-14 21:36:37.11401 INFO::Processing subtree level 1
2024-07-14 21:36:39.536995 INFO::Processing subtree level 2
2024-07-14 21:36:41.848126 INFO::Adjusting the last 1 batches sequentially
2024-07-14 21:36:41.849819 INFO::Done
2024-07-14 21:36:41.850626 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:41.856615 INFO::ASW Batch was 0.48070606416095 prior to batch effect correction and is now 0.48070606416095 .
2024-07-14 21:36:41.857408 INFO::ASW Label was 0.327066601739612 prior to batch effect correction and is now 0.327066601739612 .
2024-07-14 21:36:41.858521 INFO::Total function execution time is 4.77156805992126 s and adjustment time is 4.73783087730408 s ( 99.29 )
2024-07-14 21:36:41.859404 INFO::Formatting Data.
2024-07-14 21:36:41.860102 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:41.861156 INFO::Removing potential empty rows and columns
2024-07-14 21:36:41.863307 INFO::Found 1000 missing values.
2024-07-14 21:36:41.875516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:41.876203 INFO::Done
2024-07-14 21:36:41.876844 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:41.882717 INFO::Starting hierarchical adjustment
2024-07-14 21:36:41.883518 INFO::Found 10 batches.
2024-07-14 21:36:42.570392 INFO::Set up parallel execution backend with 2 workers
2024-07-14 21:36:42.571501 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-14 21:36:45.698447 INFO::Adjusting the last 2 batches sequentially
2024-07-14 21:36:45.700054 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-14 21:36:45.713844 INFO::Done
2024-07-14 21:36:45.714575 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:45.720117 INFO::ASW Batch was 0.48070606416095 prior to batch effect correction and is now 0.48070606416095 .
2024-07-14 21:36:45.720778 INFO::ASW Label was 0.327066601739612 prior to batch effect correction and is now 0.327066601739612 .
2024-07-14 21:36:45.721713 INFO::Total function execution time is 3.86231398582458 s and adjustment time is 3.83042812347412 s ( 99.17 )
2024-07-14 21:36:48.11316 INFO::Formatting Data.
2024-07-14 21:36:48.11405 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:48.115032 INFO::Removing potential empty rows and columns
2024-07-14 21:36:48.116062 INFO::Found 0 missing values.
2024-07-14 21:36:48.118883 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:48.119519 INFO::Done
2024-07-14 21:36:48.120159 INFO::Acquiring quality metrics before batch effect correction.
2024-07-14 21:36:48.122616 INFO::Starting hierarchical adjustment
2024-07-14 21:36:48.123432 INFO::Found 3 batches.
2024-07-14 21:36:48.124049 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-14 21:36:48.124727 INFO::Using default BPPARAM
2024-07-14 21:36:48.125345 INFO::Processing subtree level 1
2024-07-14 21:36:51.012865 INFO::Adjusting the last 1 batches sequentially
2024-07-14 21:36:51.014961 INFO::Done
2024-07-14 21:36:51.015841 INFO::Acquiring quality metrics after batch effect correction.
2024-07-14 21:36:51.018391 INFO::ASW Batch was 0.135779120951757 prior to batch effect correction and is now -0.131128469039684 .
2024-07-14 21:36:51.01906 INFO::ASW Label was -0.187427657703645 prior to batch effect correction and is now 0.0668356985386956 .
2024-07-14 21:36:51.019915 INFO::Total function execution time is 2.9068489074707 s and adjustment time is 2.89160799980164 s ( 99.48 )
2024-07-14 21:36:51.156459 INFO::Formatting Data.
2024-07-14 21:36:51.157447 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.158495 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.159552 INFO::Found 2 missing values.
2024-07-14 21:36:51.161905 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.162561 INFO::Done
2024-07-14 21:36:51.201813 INFO::Found NA in Reference column
2024-07-14 21:36:51.214725 INFO::Require at least two references per batch.
2024-07-14 21:36:51.234962 INFO::Formatting Data.
2024-07-14 21:36:51.235801 INFO::Recognized SummarizedExperiment
2024-07-14 21:36:51.236464 INFO::Typecasting input to dataframe.
2024-07-14 21:36:51.243533 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.244626 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.247249 INFO::Found 0 missing values.
2024-07-14 21:36:51.252165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.252817 INFO::Done
2024-07-14 21:36:51.26819 INFO::Formatting Data.
2024-07-14 21:36:51.269157 INFO::Recognized SummarizedExperiment
2024-07-14 21:36:51.269778 INFO::Typecasting input to dataframe.
2024-07-14 21:36:51.2823 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.28346 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.286195 INFO::Found 0 missing values.
2024-07-14 21:36:51.293852 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.294553 INFO::Done
2024-07-14 21:36:51.309439 INFO::Formatting Data.
2024-07-14 21:36:51.310293 INFO::Recognized SummarizedExperiment
2024-07-14 21:36:51.311055 INFO::Typecasting input to dataframe.
2024-07-14 21:36:51.322978 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.324041 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.325101 INFO::Found 0 missing values.
2024-07-14 21:36:51.326061 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-14 21:36:51.330246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.331439 INFO::Done
2024-07-14 21:36:51.345912 INFO::Formatting Data.
2024-07-14 21:36:51.346802 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.347803 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.348817 INFO::Found 0 missing values.
2024-07-14 21:36:51.351125 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.351757 INFO::Done
2024-07-14 21:36:51.365191 INFO::Formatting Data.
2024-07-14 21:36:51.365989 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.366892 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.367873 INFO::Found 0 missing values.
2024-07-14 21:36:51.37032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.37097 INFO::Done
2024-07-14 21:36:51.410146 INFO::Formatting Data.
2024-07-14 21:36:51.411452 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.412651 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.413814 INFO::Found 1 missing values.
2024-07-14 21:36:51.415928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.416563 INFO::Done
2024-07-14 21:36:51.440556 INFO::Formatting Data.
2024-07-14 21:36:51.441405 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.442293 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.443279 INFO::Found 2 missing values.
2024-07-14 21:36:51.444258 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-14 21:36:51.44616 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.446805 INFO::Done
2024-07-14 21:36:51.459148 INFO::Formatting Data.
2024-07-14 21:36:51.459917 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.460795 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.46173 INFO::Found 2 missing values.
2024-07-14 21:36:51.463121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.463745 INFO::Done
2024-07-14 21:36:51.476695 INFO::Formatting Data.
2024-07-14 21:36:51.477624 INFO::Typecasting input to dataframe.
2024-07-14 21:36:51.478526 INFO::Replacing NaNs with NAs.
2024-07-14 21:36:51.479448 INFO::Removing potential empty rows and columns
2024-07-14 21:36:51.480437 INFO::Found 0 missing values.
2024-07-14 21:36:51.482913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-14 21:36:51.483584 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
25.45 1.70 63.45
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 6.62 | 4.11 | 17.31 | |
| compute_asw | 0.03 | 0.00 | 0.04 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0 | 0 | 0 | |