Yannis Schumann
| Snapshot Date: 2024-10-17 13:40 -0400 (Thu, 17 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-18 11:46 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
| 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 159/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-10-17 19:44:55 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 19:49:39 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 284.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 20.292 1.138 14.663
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
2024-10-17 19:49:24.071482 INFO::Formatting Data.
2024-10-17 19:49:24.074172 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:24.084319 INFO::Removing potential empty rows and columns
2024-10-17 19:49:24.301292 INFO::Found 0 missing values.
2024-10-17 19:49:24.303959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:24.30443 INFO::Done
2024-10-17 19:49:24.304845 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:24.31511 INFO::Starting hierarchical adjustment
2024-10-17 19:49:24.315776 INFO::Found 3 batches.
2024-10-17 19:49:24.316264 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:24.317162 INFO::Using default BPPARAM
2024-10-17 19:49:24.317592 INFO::Processing subtree level 1
2024-10-17 19:49:24.41406 INFO::Adjusting the last 1 batches sequentially
2024-10-17 19:49:24.418624 INFO::Done
2024-10-17 19:49:24.420596 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:24.425427 INFO::ASW Batch was 0.0922805176121139 prior to batch effect correction and is now 0.0922805176121139 .
2024-10-17 19:49:24.427142 INFO::Total function execution time is 0.355443954467773 s and adjustment time is 0.102967023849487 s ( 28.97 )
2024-10-17 19:49:24.442733 INFO::Formatting Data.
2024-10-17 19:49:24.443434 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:24.444253 INFO::Removing potential empty rows and columns
2024-10-17 19:49:24.445427 INFO::Found 0 missing values.
2024-10-17 19:49:24.446332 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.
2024-10-17 19:49:24.456684 INFO::Formatting Data.
2024-10-17 19:49:24.457339 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:24.458093 INFO::Removing potential empty rows and columns
2024-10-17 19:49:24.45895 INFO::Found 0 missing values.
2024-10-17 19:49:24.459696 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.
2024-10-17 19:49:24.475484 INFO::Formatting Data.
2024-10-17 19:49:24.476142 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:24.476928 INFO::Removing potential empty rows and columns
2024-10-17 19:49:24.477797 INFO::Found 0 missing values.
2024-10-17 19:49:24.478554 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.
2024-10-17 19:49:24.482255 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:24.482718 INFO::Done
2024-10-17 19:49:24.483162 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:24.484892 INFO::Starting hierarchical adjustment
2024-10-17 19:49:24.485504 INFO::Found 2 batches.
2024-10-17 19:49:24.485963 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:24.48654 INFO::Using default BPPARAM
2024-10-17 19:49:24.487004 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:24.48779 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:24.508342 INFO::Done
2024-10-17 19:49:24.509107 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:24.511433 INFO::ASW Batch was -0.0204034069022838 prior to batch effect correction and is now -0.0798682228789763 .
2024-10-17 19:49:24.512195 INFO::Total function execution time is 0.0367648601531982 s and adjustment time is 0.0229358673095703 s ( 62.39 )
2024-10-17 19:49:24.514968 INFO::Formatting Data.
2024-10-17 19:49:24.515574 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:24.523508 INFO::Formatting Data.
2024-10-17 19:49:24.524092 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:24.524999 INFO::Removing potential empty rows and columns
2024-10-17 19:49:24.525876 INFO::Found 0 missing values.
2024-10-17 19:49:24.528602 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:24.529097 INFO::Done
2024-10-17 19:49:24.529819 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:24.531623 INFO::Starting hierarchical adjustment
2024-10-17 19:49:24.532238 INFO::Found 2 batches.
2024-10-17 19:49:24.532722 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:24.533307 INFO::Using default BPPARAM
2024-10-17 19:49:24.533774 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:24.5346 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:24.549279 INFO::Done
2024-10-17 19:49:24.549861 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:24.551712 INFO::ASW Batch was 0.0264517312393338 prior to batch effect correction and is now -0.124314414866289 .
2024-10-17 19:49:24.55242 INFO::Total function execution time is 0.0288951396942139 s and adjustment time is 0.0171558856964111 s ( 59.37 )
2024-10-17 19:49:24.553585 INFO::Formatting Data.
2024-10-17 19:49:24.554114 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:24.554851 INFO::Removing potential empty rows and columns
2024-10-17 19:49:24.555708 INFO::Found 0 missing values.
2024-10-17 19:49:24.558042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:24.558786 INFO::Done
2024-10-17 19:49:24.559282 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:24.561069 INFO::Starting hierarchical adjustment
2024-10-17 19:49:24.56167 INFO::Found 2 batches.
2024-10-17 19:49:24.562149 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:24.562698 INFO::Using default BPPARAM
2024-10-17 19:49:24.563153 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:24.563897 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:24.576963 INFO::Done
2024-10-17 19:49:24.577548 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:24.579295 INFO::ASW Batch was 0.0264517312393338 prior to batch effect correction and is now -0.124314414866289 .
2024-10-17 19:49:24.579975 INFO::Total function execution time is 0.0263919830322266 s and adjustment time is 0.0153970718383789 s ( 58.34 )
2024-10-17 19:49:26.331506 INFO::Formatting Data.
2024-10-17 19:49:26.332049 INFO::Recognized SummarizedExperiment
2024-10-17 19:49:26.332434 INFO::Typecasting input to dataframe.
2024-10-17 19:49:26.355992 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:26.356923 INFO::Removing potential empty rows and columns
2024-10-17 19:49:26.359573 INFO::Found 0 missing values.
2024-10-17 19:49:26.364221 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:26.364648 INFO::Done
2024-10-17 19:49:26.365045 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:26.367656 INFO::Starting hierarchical adjustment
2024-10-17 19:49:26.368173 INFO::Found 2 batches.
2024-10-17 19:49:26.368554 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:26.369365 INFO::Using default BPPARAM
2024-10-17 19:49:26.369763 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:26.370518 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:26.406045 INFO::Done
2024-10-17 19:49:26.406536 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:26.408945 INFO::ASW Batch was -0.00434144796988378 prior to batch effect correction and is now -0.0866969829919049 .
2024-10-17 19:49:26.409528 INFO::Total function execution time is 0.078261137008667 s and adjustment time is 0.0379600524902344 s ( 48.5 )
2024-10-17 19:49:26.42407 INFO::Formatting Data.
2024-10-17 19:49:26.424629 INFO::Recognized SummarizedExperiment
2024-10-17 19:49:26.425038 INFO::Typecasting input to dataframe.
2024-10-17 19:49:26.431783 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:26.432684 INFO::Removing potential empty rows and columns
2024-10-17 19:49:26.435331 INFO::Found 0 missing values.
2024-10-17 19:49:26.441202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:26.441702 INFO::Done
2024-10-17 19:49:26.442138 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:26.445163 INFO::Starting hierarchical adjustment
2024-10-17 19:49:26.445752 INFO::Found 2 batches.
2024-10-17 19:49:26.44616 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:26.446614 INFO::Using default BPPARAM
2024-10-17 19:49:26.447085 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:26.448087 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:26.465716 INFO::Done
2024-10-17 19:49:26.46628 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:26.46984 INFO::ASW Batch was 0.00161315704350616 prior to batch effect correction and is now 0.00161315704350616 .
2024-10-17 19:49:26.470521 INFO::Total function execution time is 0.0464169979095459 s and adjustment time is 0.0200638771057129 s ( 43.23 )
2024-10-17 19:49:26.486978 INFO::Formatting Data.
2024-10-17 19:49:26.48759 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:26.48824 INFO::Removing potential empty rows and columns
2024-10-17 19:49:26.489041 INFO::Found 0 missing values.
2024-10-17 19:49:26.491137 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:26.491548 INFO::Done
2024-10-17 19:49:26.491951 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:26.493406 INFO::Starting hierarchical adjustment
2024-10-17 19:49:26.49393 INFO::Found 3 batches.
2024-10-17 19:49:26.49444 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:26.494976 INFO::Using default BPPARAM
2024-10-17 19:49:26.495401 INFO::Processing subtree level 1
2024-10-17 19:49:26.661527 INFO::Adjusting the last 1 batches sequentially
2024-10-17 19:49:26.665673 INFO::Done
2024-10-17 19:49:26.66715 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:26.672786 INFO::ASW Batch was -0.076051067422483 prior to batch effect correction and is now -0.173493588585333 .
2024-10-17 19:49:26.67491 INFO::Total function execution time is 0.187922954559326 s and adjustment time is 0.171810865402222 s ( 91.43 )
2024-10-17 19:49:26.694228 INFO::Skipping initial DF formatting
2024-10-17 19:49:26.694808 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:26.69791 INFO::Starting hierarchical adjustment
2024-10-17 19:49:26.698524 INFO::Found 5 batches.
2024-10-17 19:49:26.698951 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:26.69946 INFO::Using default BPPARAM
2024-10-17 19:49:26.700004 INFO::Processing subtree level 1
2024-10-17 19:49:26.827531 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:26.833485 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:26.85457 INFO::Done
2024-10-17 19:49:26.8558 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:26.861178 INFO::ASW Batch was 0.516086320832831 prior to batch effect correction and is now 0.516086320832831 .
2024-10-17 19:49:26.862117 INFO::ASW Label was 0.331176900048368 prior to batch effect correction and is now 0.331176900048369 .
2024-10-17 19:49:26.863315 INFO::Total function execution time is 0.16913914680481 s and adjustment time is 0.156147956848145 s ( 92.32 )
2024-10-17 19:49:26.884552 INFO::Formatting Data.
2024-10-17 19:49:26.885309 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:26.88676 INFO::Removing potential empty rows and columns
2024-10-17 19:49:26.887903 INFO::Found 0 missing values.
2024-10-17 19:49:26.891626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:26.892142 INFO::Done
2024-10-17 19:49:26.892622 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:26.895251 INFO::Starting hierarchical adjustment
2024-10-17 19:49:26.895893 INFO::Found 5 batches.
2024-10-17 19:49:26.896349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:26.89691 INFO::Using default BPPARAM
2024-10-17 19:49:26.897656 INFO::Processing subtree level 1
2024-10-17 19:49:27.018604 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.038442 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.06348 INFO::Done
2024-10-17 19:49:27.064445 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.068543 INFO::ASW Batch was 0.519973857707344 prior to batch effect correction and is now -0.0864724207418627 .
2024-10-17 19:49:27.069349 INFO::ASW Label was 0.194108305627829 prior to batch effect correction and is now 0.846743201805608 .
2024-10-17 19:49:27.070609 INFO::Total function execution time is 0.18603515625 s and adjustment time is 0.167618989944458 s ( 90.1 )
2024-10-17 19:49:27.071404 INFO::Formatting Data.
2024-10-17 19:49:27.071944 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.073038 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.074054 INFO::Found 0 missing values.
2024-10-17 19:49:27.077721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.078183 INFO::Done
2024-10-17 19:49:27.078643 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.081178 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.082108 INFO::Found 5 batches.
2024-10-17 19:49:27.083269 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.083799 INFO::Using default BPPARAM
2024-10-17 19:49:27.084241 INFO::Processing subtree level 1
2024-10-17 19:49:27.271536 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.273825 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.31026 INFO::Done
2024-10-17 19:49:27.311124 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.316985 INFO::ASW Batch was 0.519973857707344 prior to batch effect correction and is now -0.0864724207418627 .
2024-10-17 19:49:27.317518 INFO::ASW Label was 0.194108305627829 prior to batch effect correction and is now 0.846743201805608 .
2024-10-17 19:49:27.319352 INFO::Total function execution time is 0.247543811798096 s and adjustment time is 0.228247880935669 s ( 92.21 )
2024-10-17 19:49:27.337788 INFO::Formatting Data.
2024-10-17 19:49:27.3385 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.339332 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.340392 INFO::Found 0 missing values.
2024-10-17 19:49:27.343885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.344665 INFO::Done
2024-10-17 19:49:27.345132 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.347728 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.34837 INFO::Found 5 batches.
2024-10-17 19:49:27.348841 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.349699 INFO::Using default BPPARAM
2024-10-17 19:49:27.35047 INFO::Processing subtree level 1
2024-10-17 19:49:27.526631 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.531444 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.558451 INFO::Done
2024-10-17 19:49:27.559058 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.562305 INFO::ASW Batch was 0.518421952712794 prior to batch effect correction and is now -0.0579603354120015 .
2024-10-17 19:49:27.56281 INFO::ASW Label was 0.242557643876973 prior to batch effect correction and is now 0.772434766794714 .
2024-10-17 19:49:27.563469 INFO::Total function execution time is 0.22576904296875 s and adjustment time is 0.21018385887146 s ( 93.1 )
2024-10-17 19:49:27.564244 INFO::Formatting Data.
2024-10-17 19:49:27.564749 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.565477 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.566427 INFO::Found 0 missing values.
2024-10-17 19:49:27.570021 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.570475 INFO::Done
2024-10-17 19:49:27.571084 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.573484 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.574071 INFO::Found 5 batches.
2024-10-17 19:49:27.574495 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.575231 INFO::Using default BPPARAM
2024-10-17 19:49:27.575662 INFO::Processing subtree level 1
2024-10-17 19:49:27.707563 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.717801 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.746865 INFO::Done
2024-10-17 19:49:27.747487 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.751141 INFO::ASW Batch was 0.518421952712794 prior to batch effect correction and is now -0.0579603354120015 .
2024-10-17 19:49:27.751671 INFO::ASW Label was 0.242557643876973 prior to batch effect correction and is now 0.772434766794714 .
2024-10-17 19:49:27.752717 INFO::Total function execution time is 0.188452005386353 s and adjustment time is 0.17288613319397 s ( 91.74 )
2024-10-17 19:49:27.769486 INFO::Formatting Data.
2024-10-17 19:49:27.770194 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.771036 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.772006 INFO::Found 0 missing values.
2024-10-17 19:49:27.774805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.775316 INFO::Done
2024-10-17 19:49:27.775806 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.778364 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.779051 INFO::Found 2 batches.
2024-10-17 19:49:27.779545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.780087 INFO::Using default BPPARAM
2024-10-17 19:49:27.780546 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.78136 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.795644 INFO::Done
2024-10-17 19:49:27.7962 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.799024 INFO::ASW Batch was 0.512129365796 prior to batch effect correction and is now -0.0359571116175472 .
2024-10-17 19:49:27.799606 INFO::ASW Label was 0.567114801429072 prior to batch effect correction and is now 0.932049827342482 .
2024-10-17 19:49:27.800354 INFO::Total function execution time is 0.0309579372406006 s and adjustment time is 0.016726016998291 s ( 54.03 )
2024-10-17 19:49:27.801402 INFO::Formatting Data.
2024-10-17 19:49:27.801937 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.802703 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.803507 INFO::Found 0 missing values.
2024-10-17 19:49:27.805834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.806286 INFO::Done
2024-10-17 19:49:27.806709 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.809276 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.809859 INFO::Found 2 batches.
2024-10-17 19:49:27.810275 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.810772 INFO::Using default BPPARAM
2024-10-17 19:49:27.811312 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.812262 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.825732 INFO::Done
2024-10-17 19:49:27.826279 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.828802 INFO::ASW Batch was 0.512129365796 prior to batch effect correction and is now -0.0359571116175472 .
2024-10-17 19:49:27.829329 INFO::ASW Label was 0.567114801429072 prior to batch effect correction and is now 0.932049827342482 .
2024-10-17 19:49:27.830042 INFO::Total function execution time is 0.0286350250244141 s and adjustment time is 0.01596999168396 s ( 55.77 )
2024-10-17 19:49:27.84285 INFO::Formatting Data.
2024-10-17 19:49:27.843558 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.844349 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.845172 INFO::Found 0 missing values.
2024-10-17 19:49:27.847064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.84757 INFO::Done
2024-10-17 19:49:27.848042 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.849798 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.850422 INFO::Found 2 batches.
2024-10-17 19:49:27.850851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.851342 INFO::Using default BPPARAM
2024-10-17 19:49:27.851886 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.85263 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.880692 INFO::Done
2024-10-17 19:49:27.881306 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.882929 INFO::ASW Batch was -0.0652939262043527 prior to batch effect correction and is now -0.124105911321781 .
2024-10-17 19:49:27.883571 INFO::Total function execution time is 0.0407941341400146 s and adjustment time is 0.0303678512573242 s ( 74.44 )
2024-10-17 19:49:27.897566 INFO::Formatting Data.
2024-10-17 19:49:27.898243 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.89901 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.899845 INFO::Found 0 missing values.
2024-10-17 19:49:27.900884 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.
2024-10-17 19:49:27.905025 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.905467 INFO::Done
2024-10-17 19:49:27.905895 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.908183 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.908732 INFO::Found 2 batches.
2024-10-17 19:49:27.909142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.909624 INFO::Using default BPPARAM
2024-10-17 19:49:27.91008 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.910873 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.924745 INFO::Done
2024-10-17 19:49:27.925276 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.927716 INFO::ASW Batch was 0.515959979004154 prior to batch effect correction and is now 0.0784883074134251 .
2024-10-17 19:49:27.928237 INFO::ASW Label was 0.589471995644939 prior to batch effect correction and is now 0.864983140533339 .
2024-10-17 19:49:27.928905 INFO::Total function execution time is 0.0314359664916992 s and adjustment time is 0.0161168575286865 s ( 51.27 )
2024-10-17 19:49:27.929542 INFO::Formatting Data.
2024-10-17 19:49:27.930032 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:27.930755 INFO::Removing potential empty rows and columns
2024-10-17 19:49:27.931731 INFO::Found 0 missing values.
2024-10-17 19:49:27.932517 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.
2024-10-17 19:49:27.935977 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:27.936388 INFO::Done
2024-10-17 19:49:27.936787 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:27.93896 INFO::Starting hierarchical adjustment
2024-10-17 19:49:27.939493 INFO::Found 2 batches.
2024-10-17 19:49:27.939885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:27.940337 INFO::Using default BPPARAM
2024-10-17 19:49:27.940754 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:27.941696 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:27.955819 INFO::Done
2024-10-17 19:49:27.956384 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:27.958907 INFO::ASW Batch was 0.515959979004154 prior to batch effect correction and is now 0.0784883074134251 .
2024-10-17 19:49:27.959398 INFO::ASW Label was 0.589471995644939 prior to batch effect correction and is now 0.864983140533339 .
2024-10-17 19:49:27.960078 INFO::Total function execution time is 0.0305471420288086 s and adjustment time is 0.0164170265197754 s ( 53.74 )
2024-10-17 19:49:28.130854 INFO::Formatting Data.
2024-10-17 19:49:28.131504 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:28.132242 INFO::Removing potential empty rows and columns
2024-10-17 19:49:28.133038 INFO::Found 0 missing values.
2024-10-17 19:49:28.144696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:28.145231 INFO::Done
2024-10-17 19:49:28.145664 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:28.14742 INFO::Starting hierarchical adjustment
2024-10-17 19:49:28.148021 INFO::Found 3 batches.
2024-10-17 19:49:28.14846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:28.148943 INFO::Using default BPPARAM
2024-10-17 19:49:28.149378 INFO::Processing subtree level 1
2024-10-17 19:49:28.270294 INFO::Adjusting the last 1 batches sequentially
2024-10-17 19:49:28.276578 INFO::Done
2024-10-17 19:49:28.279874 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:28.288428 INFO::ASW Batch was -0.110848315007996 prior to batch effect correction and is now -0.110848315007996 .
2024-10-17 19:49:28.290386 INFO::Total function execution time is 0.159507989883423 s and adjustment time is 0.128647089004517 s ( 80.65 )
2024-10-17 19:49:28.291753 INFO::Formatting Data.
2024-10-17 19:49:28.292342 INFO::Typecasting input to dataframe.
2024-10-17 19:49:28.293259 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:28.294606 INFO::Removing potential empty rows and columns
2024-10-17 19:49:28.295885 INFO::Found 0 missing values.
2024-10-17 19:49:28.299562 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:28.299998 INFO::Done
2024-10-17 19:49:28.300489 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:28.302894 INFO::Starting hierarchical adjustment
2024-10-17 19:49:28.303503 INFO::Found 3 batches.
2024-10-17 19:49:28.303934 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:28.304438 INFO::Using default BPPARAM
2024-10-17 19:49:28.304918 INFO::Processing subtree level 1
2024-10-17 19:49:28.423812 INFO::Adjusting the last 1 batches sequentially
2024-10-17 19:49:28.42835 INFO::Done
2024-10-17 19:49:28.430272 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:28.436268 INFO::ASW Batch was -0.110848315007996 prior to batch effect correction and is now -0.110848315007996 .
2024-10-17 19:49:28.438934 INFO::Total function execution time is 0.14709997177124 s and adjustment time is 0.124939918518066 s ( 84.94 )
2024-10-17 19:49:28.458372 INFO::Formatting Data.
2024-10-17 19:49:28.459097 INFO::Typecasting input to dataframe.
2024-10-17 19:49:28.459868 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:28.461907 INFO::Removing potential empty rows and columns
2024-10-17 19:49:28.463554 INFO::Found 0 missing values.
2024-10-17 19:49:28.468165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:28.468964 INFO::Done
2024-10-17 19:49:28.46942 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:28.471143 INFO::Starting hierarchical adjustment
2024-10-17 19:49:28.471736 INFO::Found 3 batches.
2024-10-17 19:49:28.472186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:28.473115 INFO::Using default BPPARAM
2024-10-17 19:49:28.473564 INFO::Processing subtree level 1
2024-10-17 19:49:28.591173 INFO::Adjusting the last 1 batches sequentially
2024-10-17 19:49:28.595836 INFO::Done
2024-10-17 19:49:28.597564 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:28.603557 INFO::ASW Batch was -0.0919609371684123 prior to batch effect correction and is now -0.0919609371684123 .
2024-10-17 19:49:28.605613 INFO::Total function execution time is 0.147384881973267 s and adjustment time is 0.124186038970947 s ( 84.26 )
2024-10-17 19:49:28.802707 INFO::Formatting Data.
2024-10-17 19:49:28.803487 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:28.805197 INFO::Removing potential empty rows and columns
2024-10-17 19:49:28.807595 INFO::Found 1000 missing values.
2024-10-17 19:49:28.825474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:28.826058 INFO::Done
2024-10-17 19:49:28.826507 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:28.830849 INFO::Starting hierarchical adjustment
2024-10-17 19:49:28.831535 INFO::Found 10 batches.
2024-10-17 19:49:28.832015 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:28.832578 INFO::Using default BPPARAM
2024-10-17 19:49:28.833001 INFO::Processing subtree level 1
2024-10-17 19:49:28.985976 INFO::Processing subtree level 2
2024-10-17 19:49:29.171715 INFO::Adjusting the last 1 batches sequentially
2024-10-17 19:49:29.178644 INFO::Done
2024-10-17 19:49:29.179521 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:29.18741 INFO::ASW Batch was 0.478722324831399 prior to batch effect correction and is now 0.478722324831399 .
2024-10-17 19:49:29.188618 INFO::ASW Label was 0.346897586380522 prior to batch effect correction and is now 0.346897586380522 .
2024-10-17 19:49:29.190638 INFO::Total function execution time is 0.387731075286865 s and adjustment time is 0.347215175628662 s ( 89.55 )
2024-10-17 19:49:29.191843 INFO::Formatting Data.
2024-10-17 19:49:29.192649 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:29.194217 INFO::Removing potential empty rows and columns
2024-10-17 19:49:29.197359 INFO::Found 1000 missing values.
2024-10-17 19:49:29.215542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:29.216186 INFO::Done
2024-10-17 19:49:29.216941 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:29.22185 INFO::Starting hierarchical adjustment
2024-10-17 19:49:29.222538 INFO::Found 10 batches.
2024-10-17 19:49:30.039016 INFO::Set up parallel execution backend with 2 workers
2024-10-17 19:49:30.039627 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-17 19:49:30.985109 INFO::Adjusting the last 2 batches sequentially
2024-10-17 19:49:30.986228 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 19:49:30.99904 INFO::Done
2024-10-17 19:49:30.999556 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:31.003504 INFO::ASW Batch was 0.478722324831399 prior to batch effect correction and is now 0.478722324831399 .
2024-10-17 19:49:31.003969 INFO::ASW Label was 0.346897586380522 prior to batch effect correction and is now 0.346897586380522 .
2024-10-17 19:49:31.004519 INFO::Total function execution time is 1.81272983551025 s and adjustment time is 1.77663397789001 s ( 98.01 )
2024-10-17 19:49:31.158964 INFO::Formatting Data.
2024-10-17 19:49:31.159624 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.160852 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.16186 INFO::Found 0 missing values.
2024-10-17 19:49:31.164666 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.16507 INFO::Done
2024-10-17 19:49:31.165464 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 19:49:31.168309 INFO::Starting hierarchical adjustment
2024-10-17 19:49:31.16895 INFO::Found 3 batches.
2024-10-17 19:49:31.16947 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 19:49:31.169992 INFO::Using default BPPARAM
2024-10-17 19:49:31.170452 INFO::Processing subtree level 1
2024-10-17 19:49:31.27717 INFO::Adjusting the last 1 batches sequentially
2024-10-17 19:49:31.282571 INFO::Done
2024-10-17 19:49:31.283229 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 19:49:31.291255 INFO::ASW Batch was 0.17376127957168 prior to batch effect correction and is now -0.131195952472393 .
2024-10-17 19:49:31.292213 INFO::ASW Label was -0.190437812010057 prior to batch effect correction and is now -0.0383017164143528 .
2024-10-17 19:49:31.294221 INFO::Total function execution time is 0.134949922561646 s and adjustment time is 0.113712072372437 s ( 84.26 )
2024-10-17 19:49:31.426522 INFO::Formatting Data.
2024-10-17 19:49:31.427225 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.430845 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.432514 INFO::Found 2 missing values.
2024-10-17 19:49:31.436538 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.436954 INFO::Done
2024-10-17 19:49:31.470867 INFO::Found NA in Reference column
2024-10-17 19:49:31.482114 INFO::Require at least two references per batch.
2024-10-17 19:49:31.502742 INFO::Formatting Data.
2024-10-17 19:49:31.503381 INFO::Recognized SummarizedExperiment
2024-10-17 19:49:31.503839 INFO::Typecasting input to dataframe.
2024-10-17 19:49:31.512709 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.513897 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.516872 INFO::Found 0 missing values.
2024-10-17 19:49:31.522222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.522707 INFO::Done
2024-10-17 19:49:31.536647 INFO::Formatting Data.
2024-10-17 19:49:31.53728 INFO::Recognized SummarizedExperiment
2024-10-17 19:49:31.53787 INFO::Typecasting input to dataframe.
2024-10-17 19:49:31.551995 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.552975 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.555793 INFO::Found 0 missing values.
2024-10-17 19:49:31.565223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.565834 INFO::Done
2024-10-17 19:49:31.579497 INFO::Formatting Data.
2024-10-17 19:49:31.580236 INFO::Recognized SummarizedExperiment
2024-10-17 19:49:31.580724 INFO::Typecasting input to dataframe.
2024-10-17 19:49:31.594663 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.595589 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.596494 INFO::Found 0 missing values.
2024-10-17 19:49:31.597298 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.
2024-10-17 19:49:31.601605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.602125 INFO::Done
2024-10-17 19:49:31.613346 INFO::Formatting Data.
2024-10-17 19:49:31.614003 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.614774 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.615663 INFO::Found 0 missing values.
2024-10-17 19:49:31.618256 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.618758 INFO::Done
2024-10-17 19:49:31.631537 INFO::Formatting Data.
2024-10-17 19:49:31.632247 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.633052 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.633966 INFO::Found 0 missing values.
2024-10-17 19:49:31.636281 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.636683 INFO::Done
2024-10-17 19:49:31.669383 INFO::Formatting Data.
2024-10-17 19:49:31.670058 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.670952 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.671928 INFO::Found 1 missing values.
2024-10-17 19:49:31.674241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.674706 INFO::Done
2024-10-17 19:49:31.695558 INFO::Formatting Data.
2024-10-17 19:49:31.69623 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.696963 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.69771 INFO::Found 2 missing values.
2024-10-17 19:49:31.698413 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.
2024-10-17 19:49:31.700217 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.70068 INFO::Done
2024-10-17 19:49:31.7119 INFO::Formatting Data.
2024-10-17 19:49:31.712604 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.71342 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.714289 INFO::Found 2 missing values.
2024-10-17 19:49:31.715735 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.716258 INFO::Done
2024-10-17 19:49:31.728445 INFO::Formatting Data.
2024-10-17 19:49:31.729101 INFO::Typecasting input to dataframe.
2024-10-17 19:49:31.72982 INFO::Replacing NaNs with NAs.
2024-10-17 19:49:31.730603 INFO::Removing potential empty rows and columns
2024-10-17 19:49:31.731482 INFO::Found 0 missing values.
2024-10-17 19:49:31.733921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 19:49:31.734377 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
14.189 2.971 17.311
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 20.292 | 1.138 | 14.663 | |
| compute_asw | 0.020 | 0.001 | 0.022 | |
| count_existing | 0.011 | 0.001 | 0.012 | |
| generate_data_covariables | 0.011 | 0.001 | 0.011 | |
| generate_dataset | 0.009 | 0.001 | 0.010 | |