Yannis Schumann
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
| 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 154/2239 | 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 | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2024-06-10 00:13:37 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 00:16:11 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 153.7 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* 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 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 45.768 2.62 37.256
* 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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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")
2024-06-10 00:15:32.182358 INFO::Formatting Data.
2024-06-10 00:15:32.189381 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:32.226243 INFO::Removing potential empty rows and columns
2024-06-10 00:15:33.107923 INFO::Found 0 missing values.
2024-06-10 00:15:33.14002 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:33.141689 INFO::Done
2024-06-10 00:15:33.145809 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:33.180339 INFO::Starting hierarchical adjustment
2024-06-10 00:15:33.182436 INFO::Found 3 batches.
2024-06-10 00:15:33.184073 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:33.191681 INFO::Using default BPPARAM
2024-06-10 00:15:33.193213 INFO::Processing subtree level 1
2024-06-10 00:15:33.495684 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:15:33.502932 INFO::Done
2024-06-10 00:15:33.504595 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:33.511619 INFO::ASW Batch was -0.0843034645190338 prior to batch effect correction and is now -0.0843034645190338 .
2024-06-10 00:15:33.51501 INFO::Total function execution time is 1.33374404907227 s and adjustment time is 0.321033954620361 s ( 24.07 )
2024-06-10 00:15:33.559663 INFO::Formatting Data.
2024-06-10 00:15:33.561516 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:33.564201 INFO::Removing potential empty rows and columns
2024-06-10 00:15:33.568187 INFO::Found 0 missing values.
2024-06-10 00:15:33.570891 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-10 00:15:33.600673 INFO::Formatting Data.
2024-06-10 00:15:33.602385 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:33.604571 INFO::Removing potential empty rows and columns
2024-06-10 00:15:33.607402 INFO::Found 0 missing values.
2024-06-10 00:15:33.609864 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-10 00:15:33.657679 INFO::Formatting Data.
2024-06-10 00:15:33.659377 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:33.661474 INFO::Removing potential empty rows and columns
2024-06-10 00:15:33.664141 INFO::Found 0 missing values.
2024-06-10 00:15:33.666568 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-10 00:15:33.68939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:33.691115 INFO::Done
2024-06-10 00:15:33.692525 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:33.69891 INFO::Starting hierarchical adjustment
2024-06-10 00:15:33.700726 INFO::Found 2 batches.
2024-06-10 00:15:33.702202 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:33.703928 INFO::Using default BPPARAM
2024-06-10 00:15:33.705413 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:33.708093 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:33.774513 INFO::Done
2024-06-10 00:15:33.779275 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:33.786175 INFO::ASW Batch was 0.0217516957954456 prior to batch effect correction and is now -0.0950955041158208 .
2024-06-10 00:15:33.788488 INFO::Total function execution time is 0.130777835845947 s and adjustment time is 0.074152946472168 s ( 56.7 )
2024-06-10 00:15:33.796711 INFO::Formatting Data.
2024-06-10 00:15:33.798376 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:33.832998 INFO::Formatting Data.
2024-06-10 00:15:33.834623 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:33.838356 INFO::Removing potential empty rows and columns
2024-06-10 00:15:33.841259 INFO::Found 0 missing values.
2024-06-10 00:15:33.855269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:33.856748 INFO::Done
2024-06-10 00:15:33.860531 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:33.866534 INFO::Starting hierarchical adjustment
2024-06-10 00:15:33.868883 INFO::Found 2 batches.
2024-06-10 00:15:33.870292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:33.875586 INFO::Using default BPPARAM
2024-06-10 00:15:33.878515 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:33.882368 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:33.947179 INFO::Done
2024-06-10 00:15:33.952689 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:33.957518 INFO::ASW Batch was 0.0144276851194202 prior to batch effect correction and is now -0.0976169203484122 .
2024-06-10 00:15:33.959516 INFO::Total function execution time is 0.126610994338989 s and adjustment time is 0.0786969661712646 s ( 62.16 )
2024-06-10 00:15:33.96523 INFO::Formatting Data.
2024-06-10 00:15:33.97251 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:33.974659 INFO::Removing potential empty rows and columns
2024-06-10 00:15:33.977335 INFO::Found 0 missing values.
2024-06-10 00:15:33.988264 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:33.989688 INFO::Done
2024-06-10 00:15:33.990943 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:34.000216 INFO::Starting hierarchical adjustment
2024-06-10 00:15:34.0021 INFO::Found 2 batches.
2024-06-10 00:15:34.003432 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:34.004821 INFO::Using default BPPARAM
2024-06-10 00:15:34.008429 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:34.010835 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:34.06043 INFO::Done
2024-06-10 00:15:34.062107 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:34.070221 INFO::ASW Batch was 0.0144276851194202 prior to batch effect correction and is now -0.0976169203484122 .
2024-06-10 00:15:34.072185 INFO::Total function execution time is 0.10945200920105 s and adjustment time is 0.0586459636688232 s ( 53.58 )
2024-06-10 00:15:40.20017 INFO::Formatting Data.
2024-06-10 00:15:40.201495 INFO::Recognized SummarizedExperiment
2024-06-10 00:15:40.202629 INFO::Typecasting input to dataframe.
2024-06-10 00:15:41.378245 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:41.380505 INFO::Removing potential empty rows and columns
2024-06-10 00:15:41.390624 INFO::Found 0 missing values.
2024-06-10 00:15:41.411539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:41.412802 INFO::Done
2024-06-10 00:15:41.41385 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:41.423697 INFO::Starting hierarchical adjustment
2024-06-10 00:15:41.4253 INFO::Found 2 batches.
2024-06-10 00:15:41.426422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:41.428424 INFO::Using default BPPARAM
2024-06-10 00:15:41.429548 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:41.431609 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:41.580431 INFO::Done
2024-06-10 00:15:41.581651 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:41.589969 INFO::ASW Batch was 0.0203346554182734 prior to batch effect correction and is now -0.0983833354169622 .
2024-06-10 00:15:41.591771 INFO::Total function execution time is 1.39241790771484 s and adjustment time is 0.155425786972046 s ( 11.16 )
2024-06-10 00:15:41.637495 INFO::Formatting Data.
2024-06-10 00:15:41.638805 INFO::Recognized SummarizedExperiment
2024-06-10 00:15:41.639851 INFO::Typecasting input to dataframe.
2024-06-10 00:15:41.663131 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:41.665447 INFO::Removing potential empty rows and columns
2024-06-10 00:15:41.67803 INFO::Found 0 missing values.
2024-06-10 00:15:41.703166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:41.706242 INFO::Done
2024-06-10 00:15:41.707521 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:41.715604 INFO::Starting hierarchical adjustment
2024-06-10 00:15:41.718268 INFO::Found 2 batches.
2024-06-10 00:15:41.719537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:41.720885 INFO::Using default BPPARAM
2024-06-10 00:15:41.72205 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:41.725307 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:41.799473 INFO::Done
2024-06-10 00:15:41.800766 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:41.810113 INFO::ASW Batch was 0.0050458623898361 prior to batch effect correction and is now 0.0050458623898361 .
2024-06-10 00:15:41.811816 INFO::Total function execution time is 0.174242973327637 s and adjustment time is 0.0815520286560059 s ( 46.8 )
2024-06-10 00:15:41.862281 INFO::Formatting Data.
2024-06-10 00:15:41.863722 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:41.868426 INFO::Removing potential empty rows and columns
2024-06-10 00:15:41.870907 INFO::Found 0 missing values.
2024-06-10 00:15:41.879778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:41.881119 INFO::Done
2024-06-10 00:15:41.882194 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:41.886388 INFO::Starting hierarchical adjustment
2024-06-10 00:15:41.887962 INFO::Found 3 batches.
2024-06-10 00:15:41.889094 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:41.891123 INFO::Using default BPPARAM
2024-06-10 00:15:41.892281 INFO::Processing subtree level 1
2024-06-10 00:15:42.367144 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:15:42.374977 INFO::Done
2024-06-10 00:15:42.376689 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:42.390316 INFO::ASW Batch was -0.12406623815719 prior to batch effect correction and is now -0.162227428146212 .
2024-06-10 00:15:42.397444 INFO::Total function execution time is 0.534268140792847 s and adjustment time is 0.486636161804199 s ( 91.08 )
2024-06-10 00:15:42.444834 INFO::Skipping initial DF formatting
2024-06-10 00:15:42.446876 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:42.483488 INFO::Starting hierarchical adjustment
2024-06-10 00:15:42.485471 INFO::Found 5 batches.
2024-06-10 00:15:42.486932 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:42.491396 INFO::Using default BPPARAM
2024-06-10 00:15:42.494504 INFO::Processing subtree level 1
2024-06-10 00:15:42.838125 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:42.85027 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:42.930719 INFO::Done
2024-06-10 00:15:42.933458 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:42.947003 INFO::ASW Batch was 0.56768924324018 prior to batch effect correction and is now 0.56768924324018 .
2024-06-10 00:15:42.948643 INFO::ASW Label was 0.342422774015712 prior to batch effect correction and is now 0.342422774015712 .
2024-06-10 00:15:42.951054 INFO::Total function execution time is 0.506258964538574 s and adjustment time is 0.445621013641357 s ( 88.02 )
2024-06-10 00:15:43.003091 INFO::Formatting Data.
2024-06-10 00:15:43.004796 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:43.006997 INFO::Removing potential empty rows and columns
2024-06-10 00:15:43.009641 INFO::Found 0 missing values.
2024-06-10 00:15:43.021861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:43.023592 INFO::Done
2024-06-10 00:15:43.024995 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:43.032532 INFO::Starting hierarchical adjustment
2024-06-10 00:15:43.034995 INFO::Found 5 batches.
2024-06-10 00:15:43.036545 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:43.038266 INFO::Using default BPPARAM
2024-06-10 00:15:43.039677 INFO::Processing subtree level 1
2024-06-10 00:15:43.316025 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:43.328537 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:43.382033 INFO::Done
2024-06-10 00:15:43.384058 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:43.392715 INFO::ASW Batch was 0.387950371657981 prior to batch effect correction and is now -0.0827982171429143 .
2024-06-10 00:15:43.394303 INFO::ASW Label was 0.310839471185477 prior to batch effect correction and is now 0.873064009963456 .
2024-06-10 00:15:43.396319 INFO::Total function execution time is 0.393260955810547 s and adjustment time is 0.347491979598999 s ( 88.36 )
2024-06-10 00:15:43.398744 INFO::Formatting Data.
2024-06-10 00:15:43.400892 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:43.403154 INFO::Removing potential empty rows and columns
2024-06-10 00:15:43.405801 INFO::Found 0 missing values.
2024-06-10 00:15:43.419725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:43.4219 INFO::Done
2024-06-10 00:15:43.424868 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:43.435675 INFO::Starting hierarchical adjustment
2024-06-10 00:15:43.437791 INFO::Found 5 batches.
2024-06-10 00:15:43.439446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:43.441767 INFO::Using default BPPARAM
2024-06-10 00:15:43.44338 INFO::Processing subtree level 1
2024-06-10 00:15:43.718947 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:43.727891 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:43.781392 INFO::Done
2024-06-10 00:15:43.783791 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:43.792301 INFO::ASW Batch was 0.387950371657981 prior to batch effect correction and is now -0.0827982171429143 .
2024-06-10 00:15:43.795419 INFO::ASW Label was 0.310839471185477 prior to batch effect correction and is now 0.873064009963456 .
2024-06-10 00:15:43.797848 INFO::Total function execution time is 0.399123907089233 s and adjustment time is 0.344072103500366 s ( 86.21 )
2024-06-10 00:15:43.840187 INFO::Formatting Data.
2024-06-10 00:15:43.841855 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:43.84414 INFO::Removing potential empty rows and columns
2024-06-10 00:15:43.846835 INFO::Found 0 missing values.
2024-06-10 00:15:43.857812 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:43.85984 INFO::Done
2024-06-10 00:15:43.861546 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:43.869336 INFO::Starting hierarchical adjustment
2024-06-10 00:15:43.871908 INFO::Found 5 batches.
2024-06-10 00:15:43.873334 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:43.874835 INFO::Using default BPPARAM
2024-06-10 00:15:43.876121 INFO::Processing subtree level 1
2024-06-10 00:15:44.15766 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:44.168456 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:44.227076 INFO::Done
2024-06-10 00:15:44.229184 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:44.236961 INFO::ASW Batch was 0.352581560399149 prior to batch effect correction and is now -0.0895061592049319 .
2024-06-10 00:15:44.239095 INFO::ASW Label was 0.364132371082277 prior to batch effect correction and is now 0.817517686014947 .
2024-06-10 00:15:44.241454 INFO::Total function execution time is 0.401398897171021 s and adjustment time is 0.355612993240356 s ( 88.59 )
2024-06-10 00:15:44.243612 INFO::Formatting Data.
2024-06-10 00:15:44.245245 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:44.247488 INFO::Removing potential empty rows and columns
2024-06-10 00:15:44.250101 INFO::Found 0 missing values.
2024-06-10 00:15:44.261269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:44.262704 INFO::Done
2024-06-10 00:15:44.264289 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:44.272957 INFO::Starting hierarchical adjustment
2024-06-10 00:15:44.275123 INFO::Found 5 batches.
2024-06-10 00:15:44.276507 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:44.27813 INFO::Using default BPPARAM
2024-06-10 00:15:44.280016 INFO::Processing subtree level 1
2024-06-10 00:15:44.548349 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:44.560819 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:44.622391 INFO::Done
2024-06-10 00:15:44.624764 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:44.633395 INFO::ASW Batch was 0.352581560399149 prior to batch effect correction and is now -0.0895061592049319 .
2024-06-10 00:15:44.635022 INFO::ASW Label was 0.364132371082277 prior to batch effect correction and is now 0.817517686014947 .
2024-06-10 00:15:44.637334 INFO::Total function execution time is 0.393666982650757 s and adjustment time is 0.347733020782471 s ( 88.33 )
2024-06-10 00:15:44.684256 INFO::Formatting Data.
2024-06-10 00:15:44.685975 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:44.688276 INFO::Removing potential empty rows and columns
2024-06-10 00:15:44.693653 INFO::Found 0 missing values.
2024-06-10 00:15:44.701593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:44.703587 INFO::Done
2024-06-10 00:15:44.705306 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:44.712956 INFO::Starting hierarchical adjustment
2024-06-10 00:15:44.715224 INFO::Found 2 batches.
2024-06-10 00:15:44.716673 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:44.71832 INFO::Using default BPPARAM
2024-06-10 00:15:44.719692 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:44.722015 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:44.763865 INFO::Done
2024-06-10 00:15:44.767084 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:44.775548 INFO::ASW Batch was 0.34589471566837 prior to batch effect correction and is now 0.0584171481117718 .
2024-06-10 00:15:44.777241 INFO::ASW Label was 0.714315606209211 prior to batch effect correction and is now 0.877445325357767 .
2024-06-10 00:15:44.779653 INFO::Total function execution time is 0.0954768657684326 s and adjustment time is 0.0490539073944092 s ( 51.38 )
2024-06-10 00:15:44.783561 INFO::Formatting Data.
2024-06-10 00:15:44.78514 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:44.787206 INFO::Removing potential empty rows and columns
2024-06-10 00:15:44.789934 INFO::Found 0 missing values.
2024-06-10 00:15:44.80028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:44.802126 INFO::Done
2024-06-10 00:15:44.804312 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:44.811715 INFO::Starting hierarchical adjustment
2024-06-10 00:15:44.813406 INFO::Found 2 batches.
2024-06-10 00:15:44.814569 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:44.81996 INFO::Using default BPPARAM
2024-06-10 00:15:44.821434 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:44.823796 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:44.866448 INFO::Done
2024-06-10 00:15:44.867951 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:44.877749 INFO::ASW Batch was 0.34589471566837 prior to batch effect correction and is now 0.0584171481117718 .
2024-06-10 00:15:44.879285 INFO::ASW Label was 0.714315606209211 prior to batch effect correction and is now 0.877445325357767 .
2024-06-10 00:15:44.881246 INFO::Total function execution time is 0.0977518558502197 s and adjustment time is 0.0533261299133301 s ( 54.55 )
2024-06-10 00:15:44.918227 INFO::Formatting Data.
2024-06-10 00:15:44.919884 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:44.925634 INFO::Removing potential empty rows and columns
2024-06-10 00:15:44.929221 INFO::Found 0 missing values.
2024-06-10 00:15:44.935995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:44.937435 INFO::Done
2024-06-10 00:15:44.938701 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:44.944263 INFO::Starting hierarchical adjustment
2024-06-10 00:15:44.946151 INFO::Found 2 batches.
2024-06-10 00:15:44.947493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:44.94899 INFO::Using default BPPARAM
2024-06-10 00:15:44.950308 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:44.952549 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:45.049597 INFO::Done
2024-06-10 00:15:45.051183 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:45.055965 INFO::ASW Batch was 0.00505988297663205 prior to batch effect correction and is now -0.162189472901341 .
2024-06-10 00:15:45.058089 INFO::Total function execution time is 0.139940977096558 s and adjustment time is 0.103785991668701 s ( 74.16 )
2024-06-10 00:15:45.1022 INFO::Formatting Data.
2024-06-10 00:15:45.104018 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:45.106751 INFO::Removing potential empty rows and columns
2024-06-10 00:15:45.110069 INFO::Found 0 missing values.
2024-06-10 00:15:45.113058 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-10 00:15:45.127569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:45.129455 INFO::Done
2024-06-10 00:15:45.131035 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:45.139297 INFO::Starting hierarchical adjustment
2024-06-10 00:15:45.141296 INFO::Found 2 batches.
2024-06-10 00:15:45.142743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:45.144317 INFO::Using default BPPARAM
2024-06-10 00:15:45.145567 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:45.148102 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:45.202793 INFO::Done
2024-06-10 00:15:45.204254 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:45.213627 INFO::ASW Batch was 0.597126674817541 prior to batch effect correction and is now 0.0243498692933331 .
2024-06-10 00:15:45.215247 INFO::ASW Label was 0.456643258327862 prior to batch effect correction and is now 0.845739236186587 .
2024-06-10 00:15:45.217183 INFO::Total function execution time is 0.11511492729187 s and adjustment time is 0.0618860721588135 s ( 53.76 )
2024-06-10 00:15:45.219131 INFO::Formatting Data.
2024-06-10 00:15:45.220742 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:45.223436 INFO::Removing potential empty rows and columns
2024-06-10 00:15:45.226251 INFO::Found 0 missing values.
2024-06-10 00:15:45.228731 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-10 00:15:45.244755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:45.246987 INFO::Done
2024-06-10 00:15:45.248322 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:45.255166 INFO::Starting hierarchical adjustment
2024-06-10 00:15:45.258185 INFO::Found 2 batches.
2024-06-10 00:15:45.259557 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:45.261012 INFO::Using default BPPARAM
2024-06-10 00:15:45.262322 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:45.264762 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:45.318178 INFO::Done
2024-06-10 00:15:45.319696 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:45.32697 INFO::ASW Batch was 0.597126674817541 prior to batch effect correction and is now 0.0243498692933331 .
2024-06-10 00:15:45.329402 INFO::ASW Label was 0.456643258327862 prior to batch effect correction and is now 0.845739236186587 .
2024-06-10 00:15:45.331462 INFO::Total function execution time is 0.112390041351318 s and adjustment time is 0.0603880882263184 s ( 53.73 )
2024-06-10 00:15:46.026176 INFO::Formatting Data.
2024-06-10 00:15:46.027939 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:46.033402 INFO::Removing potential empty rows and columns
2024-06-10 00:15:46.036255 INFO::Found 0 missing values.
2024-06-10 00:15:46.046477 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:46.048043 INFO::Done
2024-06-10 00:15:46.049462 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:46.05462 INFO::Starting hierarchical adjustment
2024-06-10 00:15:46.057693 INFO::Found 3 batches.
2024-06-10 00:15:46.059139 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:46.060833 INFO::Using default BPPARAM
2024-06-10 00:15:46.062393 INFO::Processing subtree level 1
2024-06-10 00:15:46.30682 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:15:46.315737 INFO::Done
2024-06-10 00:15:46.319026 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:46.334959 INFO::ASW Batch was -0.125303404333792 prior to batch effect correction and is now -0.125303404333792 .
2024-06-10 00:15:46.337622 INFO::Total function execution time is 0.311482906341553 s and adjustment time is 0.258441925048828 s ( 82.97 )
2024-06-10 00:15:46.342263 INFO::Formatting Data.
2024-06-10 00:15:46.344045 INFO::Typecasting input to dataframe.
2024-06-10 00:15:46.346071 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:46.349233 INFO::Removing potential empty rows and columns
2024-06-10 00:15:46.354613 INFO::Found 0 missing values.
2024-06-10 00:15:46.366889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:46.368251 INFO::Done
2024-06-10 00:15:46.370119 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:46.374852 INFO::Starting hierarchical adjustment
2024-06-10 00:15:46.377995 INFO::Found 3 batches.
2024-06-10 00:15:46.379439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:46.380927 INFO::Using default BPPARAM
2024-06-10 00:15:46.383042 INFO::Processing subtree level 1
2024-06-10 00:15:46.628308 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:15:46.638284 INFO::Done
2024-06-10 00:15:46.640971 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:46.652474 INFO::ASW Batch was -0.125303404333792 prior to batch effect correction and is now -0.125303404333792 .
2024-06-10 00:15:46.656445 INFO::Total function execution time is 0.313515186309814 s and adjustment time is 0.261285066604614 s ( 83.34 )
2024-06-10 00:15:46.700777 INFO::Formatting Data.
2024-06-10 00:15:46.702632 INFO::Typecasting input to dataframe.
2024-06-10 00:15:46.705811 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:46.708691 INFO::Removing potential empty rows and columns
2024-06-10 00:15:46.712814 INFO::Found 0 missing values.
2024-06-10 00:15:46.721351 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:46.7228 INFO::Done
2024-06-10 00:15:46.724843 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:46.729436 INFO::Starting hierarchical adjustment
2024-06-10 00:15:46.732056 INFO::Found 3 batches.
2024-06-10 00:15:46.734438 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:46.736122 INFO::Using default BPPARAM
2024-06-10 00:15:46.737518 INFO::Processing subtree level 1
2024-06-10 00:15:46.971675 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:15:46.981751 INFO::Done
2024-06-10 00:15:46.984187 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:46.997191 INFO::ASW Batch was -0.0812913068935893 prior to batch effect correction and is now -0.0812913068935893 .
2024-06-10 00:15:47.001228 INFO::Total function execution time is 0.299937009811401 s and adjustment time is 0.250058889389038 s ( 83.37 )
2024-06-10 00:15:47.4226 INFO::Formatting Data.
2024-06-10 00:15:47.426405 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:47.429816 INFO::Removing potential empty rows and columns
2024-06-10 00:15:47.443291 INFO::Found 1000 missing values.
2024-06-10 00:15:47.516265 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:47.519133 INFO::Done
2024-06-10 00:15:47.523514 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:47.539597 INFO::Starting hierarchical adjustment
2024-06-10 00:15:47.542417 INFO::Found 10 batches.
2024-06-10 00:15:47.544624 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:47.547999 INFO::Using default BPPARAM
2024-06-10 00:15:47.550365 INFO::Processing subtree level 1
2024-06-10 00:15:47.892276 INFO::Processing subtree level 2
2024-06-10 00:15:48.33415 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:15:48.348106 INFO::Done
2024-06-10 00:15:48.351315 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:48.373211 INFO::ASW Batch was 0.446367504631698 prior to batch effect correction and is now 0.446367504631698 .
2024-06-10 00:15:48.375848 INFO::ASW Label was 0.371198468969858 prior to batch effect correction and is now 0.371198468969858 .
2024-06-10 00:15:48.379207 INFO::Total function execution time is 0.956636905670166 s and adjustment time is 0.806110143661499 s ( 84.27 )
2024-06-10 00:15:48.38138 INFO::Formatting Data.
2024-06-10 00:15:48.383019 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:48.385776 INFO::Removing potential empty rows and columns
2024-06-10 00:15:48.393846 INFO::Found 1000 missing values.
2024-06-10 00:15:48.461086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:48.462683 INFO::Done
2024-06-10 00:15:48.464682 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:48.479554 INFO::Starting hierarchical adjustment
2024-06-10 00:15:48.481671 INFO::Found 10 batches.
2024-06-10 00:15:50.019927 INFO::Set up parallel execution backend with 2 workers
2024-06-10 00:15:50.021236 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-10 00:15:52.095814 INFO::Adjusting the last 2 batches sequentially
2024-06-10 00:15:52.098303 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-10 00:15:52.152118 INFO::Done
2024-06-10 00:15:52.153407 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:52.16807 INFO::ASW Batch was 0.446367504631698 prior to batch effect correction and is now 0.446367504631698 .
2024-06-10 00:15:52.169322 INFO::ASW Label was 0.371198468969858 prior to batch effect correction and is now 0.371198468969858 .
2024-06-10 00:15:52.17098 INFO::Total function execution time is 3.78974294662476 s and adjustment time is 3.67090582847595 s ( 96.86 )
2024-06-10 00:15:52.606129 INFO::Formatting Data.
2024-06-10 00:15:52.608432 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:52.610755 INFO::Removing potential empty rows and columns
2024-06-10 00:15:52.61501 INFO::Found 0 missing values.
2024-06-10 00:15:52.627557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:52.629062 INFO::Done
2024-06-10 00:15:52.63051 INFO::Acquiring quality metrics before batch effect correction.
2024-06-10 00:15:52.638521 INFO::Starting hierarchical adjustment
2024-06-10 00:15:52.641914 INFO::Found 3 batches.
2024-06-10 00:15:52.643878 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-10 00:15:52.646519 INFO::Using default BPPARAM
2024-06-10 00:15:52.65011 INFO::Processing subtree level 1
2024-06-10 00:15:52.976936 INFO::Adjusting the last 1 batches sequentially
2024-06-10 00:15:52.986001 INFO::Done
2024-06-10 00:15:52.987568 INFO::Acquiring quality metrics after batch effect correction.
2024-06-10 00:15:53.00252 INFO::ASW Batch was 0.155489792652144 prior to batch effect correction and is now -0.16256524384058 .
2024-06-10 00:15:53.005555 INFO::ASW Label was -0.189137666983661 prior to batch effect correction and is now -0.102616327142075 .
2024-06-10 00:15:53.011418 INFO::Total function execution time is 0.403618097305298 s and adjustment time is 0.345976114273071 s ( 85.72 )
2024-06-10 00:15:53.408725 INFO::Formatting Data.
2024-06-10 00:15:53.410565 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:53.412676 INFO::Removing potential empty rows and columns
2024-06-10 00:15:53.417801 INFO::Found 2 missing values.
2024-06-10 00:15:53.426337 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:53.427846 INFO::Done
2024-06-10 00:15:53.521459 INFO::Found NA in Reference column
2024-06-10 00:15:53.548951 INFO::Require at least two references per batch.
2024-06-10 00:15:53.618139 INFO::Formatting Data.
2024-06-10 00:15:53.619669 INFO::Recognized SummarizedExperiment
2024-06-10 00:15:53.620892 INFO::Typecasting input to dataframe.
2024-06-10 00:15:53.653038 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:53.655925 INFO::Removing potential empty rows and columns
2024-06-10 00:15:53.66925 INFO::Found 0 missing values.
2024-06-10 00:15:53.695292 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:53.696845 INFO::Done
2024-06-10 00:15:53.748912 INFO::Formatting Data.
2024-06-10 00:15:53.750459 INFO::Recognized SummarizedExperiment
2024-06-10 00:15:53.751752 INFO::Typecasting input to dataframe.
2024-06-10 00:15:53.806643 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:53.811069 INFO::Removing potential empty rows and columns
2024-06-10 00:15:53.824696 INFO::Found 0 missing values.
2024-06-10 00:15:53.871455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:53.873627 INFO::Done
2024-06-10 00:15:53.921566 INFO::Formatting Data.
2024-06-10 00:15:53.923248 INFO::Recognized SummarizedExperiment
2024-06-10 00:15:53.925273 INFO::Typecasting input to dataframe.
2024-06-10 00:15:53.98285 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:53.986708 INFO::Removing potential empty rows and columns
2024-06-10 00:15:53.989638 INFO::Found 0 missing values.
2024-06-10 00:15:53.992115 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-10 00:15:54.005727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:54.007897 INFO::Done
2024-06-10 00:15:54.040376 INFO::Formatting Data.
2024-06-10 00:15:54.044855 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:54.047266 INFO::Removing potential empty rows and columns
2024-06-10 00:15:54.050171 INFO::Found 0 missing values.
2024-06-10 00:15:54.06012 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:54.061567 INFO::Done
2024-06-10 00:15:54.096294 INFO::Formatting Data.
2024-06-10 00:15:54.098131 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:54.101861 INFO::Removing potential empty rows and columns
2024-06-10 00:15:54.104643 INFO::Found 0 missing values.
2024-06-10 00:15:54.113511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:54.11503 INFO::Done
2024-06-10 00:15:54.219914 INFO::Formatting Data.
2024-06-10 00:15:54.222034 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:54.225095 INFO::Removing potential empty rows and columns
2024-06-10 00:15:54.230089 INFO::Found 1 missing values.
2024-06-10 00:15:54.240476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:54.242615 INFO::Done
2024-06-10 00:15:54.309804 INFO::Formatting Data.
2024-06-10 00:15:54.311609 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:54.315251 INFO::Removing potential empty rows and columns
2024-06-10 00:15:54.317964 INFO::Found 2 missing values.
2024-06-10 00:15:54.320276 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-06-10 00:15:54.327066 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:54.328625 INFO::Done
2024-06-10 00:15:54.363866 INFO::Formatting Data.
2024-06-10 00:15:54.365694 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:54.367882 INFO::Removing potential empty rows and columns
2024-06-10 00:15:54.371597 INFO::Found 2 missing values.
2024-06-10 00:15:54.376257 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:54.377848 INFO::Done
2024-06-10 00:15:54.412506 INFO::Formatting Data.
2024-06-10 00:15:54.414448 INFO::Typecasting input to dataframe.
2024-06-10 00:15:54.418469 INFO::Replacing NaNs with NAs.
2024-06-10 00:15:54.421033 INFO::Removing potential empty rows and columns
2024-06-10 00:15:54.424037 INFO::Found 0 missing values.
2024-06-10 00:15:54.434591 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-10 00:15:54.43608 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
36.171 6.386 49.055
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 45.768 | 2.620 | 37.256 | |
| compute_asw | 0.058 | 0.003 | 0.075 | |
| count_existing | 0.029 | 0.001 | 0.048 | |
| generate_data_covariables | 0.027 | 0.003 | 0.039 | |
| generate_dataset | 0.024 | 0.002 | 0.028 | |