Yannis Schumann
| Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 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 2024-07-24 11:40 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| 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: 2024-07-23 19:39:27 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 19:40:55 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 87.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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 12.7.1
* 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 ... 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 28.752 1.622 20.748
* 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")
2024-07-23 19:40:33.727073 INFO::Formatting Data.
2024-07-23 19:40:33.73172 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:33.747461 INFO::Removing potential empty rows and columns
2024-07-23 19:40:34.052142 INFO::Found 0 missing values.
2024-07-23 19:40:34.057258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:34.058285 INFO::Done
2024-07-23 19:40:34.059154 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:34.077353 INFO::Starting hierarchical adjustment
2024-07-23 19:40:34.078363 INFO::Found 3 batches.
2024-07-23 19:40:34.078971 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:34.080422 INFO::Using default BPPARAM
2024-07-23 19:40:34.081114 INFO::Processing subtree level 1
2024-07-23 19:40:34.260313 INFO::Adjusting the last 1 batches sequentially
2024-07-23 19:40:34.273463 INFO::Done
2024-07-23 19:40:34.276584 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:34.287232 INFO::ASW Batch was -0.00845986631448249 prior to batch effect correction and is now -0.00845986631448249 .
2024-07-23 19:40:34.288775 INFO::Total function execution time is 0.562937021255493 s and adjustment time is 0.195142984390259 s ( 34.67 )
2024-07-23 19:40:34.319467 INFO::Formatting Data.
2024-07-23 19:40:34.320349 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:34.321473 INFO::Removing potential empty rows and columns
2024-07-23 19:40:34.322566 INFO::Found 0 missing values.
2024-07-23 19:40:34.32368 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-23 19:40:34.339207 INFO::Formatting Data.
2024-07-23 19:40:34.340496 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:34.342176 INFO::Removing potential empty rows and columns
2024-07-23 19:40:34.343834 INFO::Found 0 missing values.
2024-07-23 19:40:34.344893 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-23 19:40:34.367694 INFO::Formatting Data.
2024-07-23 19:40:34.368525 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:34.369434 INFO::Removing potential empty rows and columns
2024-07-23 19:40:34.370434 INFO::Found 0 missing values.
2024-07-23 19:40:34.371299 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-23 19:40:34.375337 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:34.375898 INFO::Done
2024-07-23 19:40:34.376374 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:34.378183 INFO::Starting hierarchical adjustment
2024-07-23 19:40:34.378822 INFO::Found 2 batches.
2024-07-23 19:40:34.379282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:34.379837 INFO::Using default BPPARAM
2024-07-23 19:40:34.380297 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:34.381109 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:34.406044 INFO::Done
2024-07-23 19:40:34.406732 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:34.409132 INFO::ASW Batch was 0.0131753637626338 prior to batch effect correction and is now -0.102393111838782 .
2024-07-23 19:40:34.409903 INFO::Total function execution time is 0.0423200130462646 s and adjustment time is 0.0273051261901855 s ( 64.52 )
2024-07-23 19:40:34.413667 INFO::Formatting Data.
2024-07-23 19:40:34.414341 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:34.425143 INFO::Formatting Data.
2024-07-23 19:40:34.425922 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:34.426948 INFO::Removing potential empty rows and columns
2024-07-23 19:40:34.428343 INFO::Found 0 missing values.
2024-07-23 19:40:34.431061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:34.431841 INFO::Done
2024-07-23 19:40:34.43252 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:34.434855 INFO::Starting hierarchical adjustment
2024-07-23 19:40:34.435466 INFO::Found 2 batches.
2024-07-23 19:40:34.436088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:34.436634 INFO::Using default BPPARAM
2024-07-23 19:40:34.437091 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:34.438144 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:34.45606 INFO::Done
2024-07-23 19:40:34.457071 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:34.459775 INFO::ASW Batch was 0.0178908991102658 prior to batch effect correction and is now -0.120361827649611 .
2024-07-23 19:40:34.460639 INFO::Total function execution time is 0.0355789661407471 s and adjustment time is 0.0206780433654785 s ( 58.12 )
2024-07-23 19:40:34.461647 INFO::Formatting Data.
2024-07-23 19:40:34.462198 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:34.462984 INFO::Removing potential empty rows and columns
2024-07-23 19:40:34.463917 INFO::Found 0 missing values.
2024-07-23 19:40:34.46667 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:34.467264 INFO::Done
2024-07-23 19:40:34.467714 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:34.46957 INFO::Starting hierarchical adjustment
2024-07-23 19:40:34.470192 INFO::Found 2 batches.
2024-07-23 19:40:34.47067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:34.471205 INFO::Using default BPPARAM
2024-07-23 19:40:34.471657 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:34.472464 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:34.487072 INFO::Done
2024-07-23 19:40:34.488311 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:34.491462 INFO::ASW Batch was 0.0178908991102658 prior to batch effect correction and is now -0.120361827649611 .
2024-07-23 19:40:34.492613 INFO::Total function execution time is 0.0308749675750732 s and adjustment time is 0.016901969909668 s ( 54.74 )
2024-07-23 19:40:37.165536 INFO::Formatting Data.
2024-07-23 19:40:37.166421 INFO::Recognized SummarizedExperiment
2024-07-23 19:40:37.167147 INFO::Typecasting input to dataframe.
2024-07-23 19:40:38.033293 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:38.034752 INFO::Removing potential empty rows and columns
2024-07-23 19:40:38.038943 INFO::Found 0 missing values.
2024-07-23 19:40:38.045625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:38.046528 INFO::Done
2024-07-23 19:40:38.047051 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:38.051024 INFO::Starting hierarchical adjustment
2024-07-23 19:40:38.051725 INFO::Found 2 batches.
2024-07-23 19:40:38.052246 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:38.053881 INFO::Using default BPPARAM
2024-07-23 19:40:38.054351 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:38.055386 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:38.120883 INFO::Done
2024-07-23 19:40:38.121729 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:38.126783 INFO::ASW Batch was 0.032148313726021 prior to batch effect correction and is now -0.0968255449074042 .
2024-07-23 19:40:38.127646 INFO::Total function execution time is 0.962594985961914 s and adjustment time is 0.0692670345306396 s ( 7.2 )
2024-07-23 19:40:38.151409 INFO::Formatting Data.
2024-07-23 19:40:38.152069 INFO::Recognized SummarizedExperiment
2024-07-23 19:40:38.152499 INFO::Typecasting input to dataframe.
2024-07-23 19:40:38.162302 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:38.16396 INFO::Removing potential empty rows and columns
2024-07-23 19:40:38.166926 INFO::Found 0 missing values.
2024-07-23 19:40:38.177086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:38.177952 INFO::Done
2024-07-23 19:40:38.178705 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:38.183528 INFO::Starting hierarchical adjustment
2024-07-23 19:40:38.184541 INFO::Found 2 batches.
2024-07-23 19:40:38.185083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:38.185693 INFO::Using default BPPARAM
2024-07-23 19:40:38.186134 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:38.187465 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:38.212167 INFO::Done
2024-07-23 19:40:38.213038 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:38.217419 INFO::ASW Batch was 0.000502509461651033 prior to batch effect correction and is now 0.000502509461651033 .
2024-07-23 19:40:38.218276 INFO::Total function execution time is 0.0667979717254639 s and adjustment time is 0.0277881622314453 s ( 41.6 )
2024-07-23 19:40:38.243066 INFO::Formatting Data.
2024-07-23 19:40:38.244113 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:38.24504 INFO::Removing potential empty rows and columns
2024-07-23 19:40:38.246418 INFO::Found 0 missing values.
2024-07-23 19:40:38.250616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:38.251436 INFO::Done
2024-07-23 19:40:38.252149 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:38.254698 INFO::Starting hierarchical adjustment
2024-07-23 19:40:38.255558 INFO::Found 3 batches.
2024-07-23 19:40:38.25636 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:38.257127 INFO::Using default BPPARAM
2024-07-23 19:40:38.257585 INFO::Processing subtree level 1
2024-07-23 19:40:38.472186 INFO::Adjusting the last 1 batches sequentially
2024-07-23 19:40:38.476252 INFO::Done
2024-07-23 19:40:38.477264 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:38.481424 INFO::ASW Batch was -0.0596287866902079 prior to batch effect correction and is now -0.176820265398737 .
2024-07-23 19:40:38.483176 INFO::Total function execution time is 0.239995956420898 s and adjustment time is 0.220731019973755 s ( 91.97 )
2024-07-23 19:40:38.515491 INFO::Skipping initial DF formatting
2024-07-23 19:40:38.517071 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:38.524837 INFO::Starting hierarchical adjustment
2024-07-23 19:40:38.526518 INFO::Found 5 batches.
2024-07-23 19:40:38.5278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:38.529537 INFO::Using default BPPARAM
2024-07-23 19:40:38.530558 INFO::Processing subtree level 1
2024-07-23 19:40:38.704643 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:38.708997 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:38.746242 INFO::Done
2024-07-23 19:40:38.747338 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:38.75444 INFO::ASW Batch was 0.520017167346143 prior to batch effect correction and is now 0.520017167346143 .
2024-07-23 19:40:38.755392 INFO::ASW Label was 0.36198333689313 prior to batch effect correction and is now 0.36198333689313 .
2024-07-23 19:40:38.757022 INFO::Total function execution time is 0.241668939590454 s and adjustment time is 0.220149993896484 s ( 91.1 )
2024-07-23 19:40:38.786534 INFO::Formatting Data.
2024-07-23 19:40:38.787741 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:38.789494 INFO::Removing potential empty rows and columns
2024-07-23 19:40:38.791505 INFO::Found 0 missing values.
2024-07-23 19:40:38.798408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:38.799356 INFO::Done
2024-07-23 19:40:38.80017 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:38.804413 INFO::Starting hierarchical adjustment
2024-07-23 19:40:38.80563 INFO::Found 5 batches.
2024-07-23 19:40:38.806529 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:38.807339 INFO::Using default BPPARAM
2024-07-23 19:40:38.808202 INFO::Processing subtree level 1
2024-07-23 19:40:38.955876 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:38.964523 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:38.993655 INFO::Done
2024-07-23 19:40:38.994689 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.000678 INFO::ASW Batch was 0.294358751172598 prior to batch effect correction and is now -0.0555572016328976 .
2024-07-23 19:40:39.001735 INFO::ASW Label was 0.433050058797624 prior to batch effect correction and is now 0.86611819863873 .
2024-07-23 19:40:39.003346 INFO::Total function execution time is 0.216646909713745 s and adjustment time is 0.188194036483765 s ( 86.87 )
2024-07-23 19:40:39.004648 INFO::Formatting Data.
2024-07-23 19:40:39.005838 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.007212 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.008394 INFO::Found 0 missing values.
2024-07-23 19:40:39.013628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.014589 INFO::Done
2024-07-23 19:40:39.015449 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.019756 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.020906 INFO::Found 5 batches.
2024-07-23 19:40:39.021852 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.022916 INFO::Using default BPPARAM
2024-07-23 19:40:39.023692 INFO::Processing subtree level 1
2024-07-23 19:40:39.177055 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.183048 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.205827 INFO::Done
2024-07-23 19:40:39.207091 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.212714 INFO::ASW Batch was 0.294358751172598 prior to batch effect correction and is now -0.0555572016328976 .
2024-07-23 19:40:39.213806 INFO::ASW Label was 0.433050058797624 prior to batch effect correction and is now 0.86611819863873 .
2024-07-23 19:40:39.215391 INFO::Total function execution time is 0.21058988571167 s and adjustment time is 0.185078144073486 s ( 87.89 )
2024-07-23 19:40:39.237877 INFO::Formatting Data.
2024-07-23 19:40:39.238945 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.240047 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.241289 INFO::Found 0 missing values.
2024-07-23 19:40:39.247711 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.248713 INFO::Done
2024-07-23 19:40:39.249588 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.25381 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.254923 INFO::Found 5 batches.
2024-07-23 19:40:39.255733 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.25689 INFO::Using default BPPARAM
2024-07-23 19:40:39.25758 INFO::Processing subtree level 1
2024-07-23 19:40:39.397671 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.408406 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.432556 INFO::Done
2024-07-23 19:40:39.433299 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.437784 INFO::ASW Batch was 0.416857982211189 prior to batch effect correction and is now 0.0331465752327183 .
2024-07-23 19:40:39.438446 INFO::ASW Label was 0.328737980509463 prior to batch effect correction and is now 0.775770219025056 .
2024-07-23 19:40:39.439621 INFO::Total function execution time is 0.201605081558228 s and adjustment time is 0.177875995635986 s ( 88.23 )
2024-07-23 19:40:39.440446 INFO::Formatting Data.
2024-07-23 19:40:39.441018 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.441946 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.443381 INFO::Found 0 missing values.
2024-07-23 19:40:39.448468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.449354 INFO::Done
2024-07-23 19:40:39.450158 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.453959 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.45469 INFO::Found 5 batches.
2024-07-23 19:40:39.45533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.456009 INFO::Using default BPPARAM
2024-07-23 19:40:39.456569 INFO::Processing subtree level 1
2024-07-23 19:40:39.594135 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.60308 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.644262 INFO::Done
2024-07-23 19:40:39.646903 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.654812 INFO::ASW Batch was 0.416857982211189 prior to batch effect correction and is now 0.0331465752327183 .
2024-07-23 19:40:39.656747 INFO::ASW Label was 0.328737980509463 prior to batch effect correction and is now 0.775770219025056 .
2024-07-23 19:40:39.659494 INFO::Total function execution time is 0.217649936676025 s and adjustment time is 0.189664125442505 s ( 87.14 )
2024-07-23 19:40:39.688974 INFO::Formatting Data.
2024-07-23 19:40:39.690406 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.691884 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.693478 INFO::Found 0 missing values.
2024-07-23 19:40:39.696995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.698617 INFO::Done
2024-07-23 19:40:39.69934 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.703778 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.705784 INFO::Found 2 batches.
2024-07-23 19:40:39.706375 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.708286 INFO::Using default BPPARAM
2024-07-23 19:40:39.70911 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.71155 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.731438 INFO::Done
2024-07-23 19:40:39.734024 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.738122 INFO::ASW Batch was 0.681805925520598 prior to batch effect correction and is now -0.0275691504106973 .
2024-07-23 19:40:39.740357 INFO::ASW Label was 0.386853850573868 prior to batch effect correction and is now 0.90820162327329 .
2024-07-23 19:40:39.742534 INFO::Total function execution time is 0.0529839992523193 s and adjustment time is 0.0259690284729004 s ( 49.01 )
2024-07-23 19:40:39.744733 INFO::Formatting Data.
2024-07-23 19:40:39.745632 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.748123 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.7501 INFO::Found 0 missing values.
2024-07-23 19:40:39.754901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.756737 INFO::Done
2024-07-23 19:40:39.758132 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.761836 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.762727 INFO::Found 2 batches.
2024-07-23 19:40:39.763908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.765069 INFO::Using default BPPARAM
2024-07-23 19:40:39.765545 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.766395 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.783204 INFO::Done
2024-07-23 19:40:39.783978 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.786794 INFO::ASW Batch was 0.681805925520598 prior to batch effect correction and is now -0.0275691504106973 .
2024-07-23 19:40:39.787623 INFO::ASW Label was 0.386853850573868 prior to batch effect correction and is now 0.90820162327329 .
2024-07-23 19:40:39.788808 INFO::Total function execution time is 0.0442209243774414 s and adjustment time is 0.0206091403961182 s ( 46.6 )
2024-07-23 19:40:39.807926 INFO::Formatting Data.
2024-07-23 19:40:39.809154 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.810288 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.811331 INFO::Found 0 missing values.
2024-07-23 19:40:39.813826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.814674 INFO::Done
2024-07-23 19:40:39.815432 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.81852 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.819185 INFO::Found 2 batches.
2024-07-23 19:40:39.819675 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.820196 INFO::Using default BPPARAM
2024-07-23 19:40:39.820686 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.821508 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.859193 INFO::Done
2024-07-23 19:40:39.859834 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.861879 INFO::ASW Batch was -0.100234039322913 prior to batch effect correction and is now -0.162801690699749 .
2024-07-23 19:40:39.862951 INFO::Total function execution time is 0.0551590919494629 s and adjustment time is 0.040118932723999 s ( 72.73 )
2024-07-23 19:40:39.881667 INFO::Formatting Data.
2024-07-23 19:40:39.882609 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.883428 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.884381 INFO::Found 0 missing values.
2024-07-23 19:40:39.885481 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-23 19:40:39.891677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.892492 INFO::Done
2024-07-23 19:40:39.893011 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.896248 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.896979 INFO::Found 2 batches.
2024-07-23 19:40:39.897626 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.898189 INFO::Using default BPPARAM
2024-07-23 19:40:39.898844 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.89974 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.917638 INFO::Done
2024-07-23 19:40:39.918371 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.922508 INFO::ASW Batch was 0.334802890377021 prior to batch effect correction and is now -0.0120785820060438 .
2024-07-23 19:40:39.923495 INFO::ASW Label was 0.684772088002159 prior to batch effect correction and is now 0.929564788233298 .
2024-07-23 19:40:39.924639 INFO::Total function execution time is 0.0429749488830566 s and adjustment time is 0.020766019821167 s ( 48.32 )
2024-07-23 19:40:39.925759 INFO::Formatting Data.
2024-07-23 19:40:39.926581 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:39.927861 INFO::Removing potential empty rows and columns
2024-07-23 19:40:39.929316 INFO::Found 0 missing values.
2024-07-23 19:40:39.930722 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-23 19:40:39.937099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:39.937871 INFO::Done
2024-07-23 19:40:39.938376 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:39.941038 INFO::Starting hierarchical adjustment
2024-07-23 19:40:39.942053 INFO::Found 2 batches.
2024-07-23 19:40:39.94278 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:39.943611 INFO::Using default BPPARAM
2024-07-23 19:40:39.94434 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:39.945745 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:39.966004 INFO::Done
2024-07-23 19:40:39.966921 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:39.970744 INFO::ASW Batch was 0.334802890377021 prior to batch effect correction and is now -0.0120785820060438 .
2024-07-23 19:40:39.971616 INFO::ASW Label was 0.684772088002159 prior to batch effect correction and is now 0.929564788233298 .
2024-07-23 19:40:39.972416 INFO::Total function execution time is 0.0467751026153564 s and adjustment time is 0.0241749286651611 s ( 51.68 )
2024-07-23 19:40:40.266038 INFO::Formatting Data.
2024-07-23 19:40:40.267149 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:40.268395 INFO::Removing potential empty rows and columns
2024-07-23 19:40:40.269691 INFO::Found 0 missing values.
2024-07-23 19:40:40.274354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:40.275232 INFO::Done
2024-07-23 19:40:40.275988 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:40.278664 INFO::Starting hierarchical adjustment
2024-07-23 19:40:40.279304 INFO::Found 3 batches.
2024-07-23 19:40:40.279809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:40.280768 INFO::Using default BPPARAM
2024-07-23 19:40:40.28149 INFO::Processing subtree level 1
2024-07-23 19:40:40.408539 INFO::Adjusting the last 1 batches sequentially
2024-07-23 19:40:40.431674 INFO::Done
2024-07-23 19:40:40.434795 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:40.446042 INFO::ASW Batch was -0.0922192896721756 prior to batch effect correction and is now -0.0922192896721756 .
2024-07-23 19:40:40.450722 INFO::Total function execution time is 0.182931900024414 s and adjustment time is 0.152447938919067 s ( 83.34 )
2024-07-23 19:40:40.453402 INFO::Formatting Data.
2024-07-23 19:40:40.45496 INFO::Typecasting input to dataframe.
2024-07-23 19:40:40.455823 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:40.457545 INFO::Removing potential empty rows and columns
2024-07-23 19:40:40.460567 INFO::Found 0 missing values.
2024-07-23 19:40:40.465163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:40.46585 INFO::Done
2024-07-23 19:40:40.466495 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:40.469244 INFO::Starting hierarchical adjustment
2024-07-23 19:40:40.470531 INFO::Found 3 batches.
2024-07-23 19:40:40.471153 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:40.472486 INFO::Using default BPPARAM
2024-07-23 19:40:40.473847 INFO::Processing subtree level 1
2024-07-23 19:40:40.586296 INFO::Adjusting the last 1 batches sequentially
2024-07-23 19:40:40.613008 INFO::Done
2024-07-23 19:40:40.616888 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:40.627376 INFO::ASW Batch was -0.0922192896721756 prior to batch effect correction and is now -0.0922192896721756 .
2024-07-23 19:40:40.631709 INFO::Total function execution time is 0.177917957305908 s and adjustment time is 0.14307713508606 s ( 80.42 )
2024-07-23 19:40:40.659078 INFO::Formatting Data.
2024-07-23 19:40:40.660851 INFO::Typecasting input to dataframe.
2024-07-23 19:40:40.662533 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:40.664633 INFO::Removing potential empty rows and columns
2024-07-23 19:40:40.666587 INFO::Found 0 missing values.
2024-07-23 19:40:40.670907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:40.671515 INFO::Done
2024-07-23 19:40:40.672005 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:40.673843 INFO::Starting hierarchical adjustment
2024-07-23 19:40:40.674496 INFO::Found 3 batches.
2024-07-23 19:40:40.674989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:40.676382 INFO::Using default BPPARAM
2024-07-23 19:40:40.677098 INFO::Processing subtree level 1
2024-07-23 19:40:40.796386 INFO::Adjusting the last 1 batches sequentially
2024-07-23 19:40:40.818482 INFO::Done
2024-07-23 19:40:40.821715 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:40.843694 INFO::ASW Batch was -0.0903028755619917 prior to batch effect correction and is now -0.0903028755619917 .
2024-07-23 19:40:40.848705 INFO::Total function execution time is 0.189327955245972 s and adjustment time is 0.144006967544556 s ( 76.06 )
2024-07-23 19:40:41.10755 INFO::Formatting Data.
2024-07-23 19:40:41.108694 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:41.110255 INFO::Removing potential empty rows and columns
2024-07-23 19:40:41.113561 INFO::Found 1000 missing values.
2024-07-23 19:40:41.133521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:41.134507 INFO::Done
2024-07-23 19:40:41.135294 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:41.140844 INFO::Starting hierarchical adjustment
2024-07-23 19:40:41.142014 INFO::Found 10 batches.
2024-07-23 19:40:41.142539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:41.143117 INFO::Using default BPPARAM
2024-07-23 19:40:41.143606 INFO::Processing subtree level 1
2024-07-23 19:40:41.340214 INFO::Processing subtree level 2
2024-07-23 19:40:41.579937 INFO::Adjusting the last 1 batches sequentially
2024-07-23 19:40:41.59635 INFO::Done
2024-07-23 19:40:41.597259 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:41.612582 INFO::ASW Batch was 0.444448368807503 prior to batch effect correction and is now 0.444448368807503 .
2024-07-23 19:40:41.615278 INFO::ASW Label was 0.361343255102109 prior to batch effect correction and is now 0.361343255102109 .
2024-07-23 19:40:41.617982 INFO::Total function execution time is 0.510058879852295 s and adjustment time is 0.454408884048462 s ( 89.09 )
2024-07-23 19:40:41.619891 INFO::Formatting Data.
2024-07-23 19:40:41.621545 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:41.623102 INFO::Removing potential empty rows and columns
2024-07-23 19:40:41.628126 INFO::Found 1000 missing values.
2024-07-23 19:40:41.65463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:41.655595 INFO::Done
2024-07-23 19:40:41.656788 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:41.664823 INFO::Starting hierarchical adjustment
2024-07-23 19:40:41.666098 INFO::Found 10 batches.
2024-07-23 19:40:42.783579 INFO::Set up parallel execution backend with 2 workers
2024-07-23 19:40:42.7844 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-23 19:40:44.222662 INFO::Adjusting the last 2 batches sequentially
2024-07-23 19:40:44.224228 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-23 19:40:44.247098 INFO::Done
2024-07-23 19:40:44.247741 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:44.255925 INFO::ASW Batch was 0.444448368807503 prior to batch effect correction and is now 0.444448368807503 .
2024-07-23 19:40:44.256849 INFO::ASW Label was 0.361343255102109 prior to batch effect correction and is now 0.361343255102109 .
2024-07-23 19:40:44.257894 INFO::Total function execution time is 2.63803386688232 s and adjustment time is 2.5813159942627 s ( 97.85 )
2024-07-23 19:40:44.520877 INFO::Formatting Data.
2024-07-23 19:40:44.522844 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:44.524542 INFO::Removing potential empty rows and columns
2024-07-23 19:40:44.526185 INFO::Found 0 missing values.
2024-07-23 19:40:44.531839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:44.532909 INFO::Done
2024-07-23 19:40:44.533707 INFO::Acquiring quality metrics before batch effect correction.
2024-07-23 19:40:44.537707 INFO::Starting hierarchical adjustment
2024-07-23 19:40:44.538605 INFO::Found 3 batches.
2024-07-23 19:40:44.539551 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-23 19:40:44.540165 INFO::Using default BPPARAM
2024-07-23 19:40:44.540638 INFO::Processing subtree level 1
2024-07-23 19:40:44.706369 INFO::Adjusting the last 1 batches sequentially
2024-07-23 19:40:44.733144 INFO::Done
2024-07-23 19:40:44.734996 INFO::Acquiring quality metrics after batch effect correction.
2024-07-23 19:40:44.747983 INFO::ASW Batch was 0.186315848716053 prior to batch effect correction and is now -0.139510733383519 .
2024-07-23 19:40:44.75046 INFO::ASW Label was -0.205980705754511 prior to batch effect correction and is now -0.0976228142248772 .
2024-07-23 19:40:44.753363 INFO::Total function execution time is 0.231635093688965 s and adjustment time is 0.193979978561401 s ( 83.74 )
2024-07-23 19:40:44.948739 INFO::Formatting Data.
2024-07-23 19:40:44.949862 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:44.951238 INFO::Removing potential empty rows and columns
2024-07-23 19:40:44.952745 INFO::Found 2 missing values.
2024-07-23 19:40:44.957318 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:44.95812 INFO::Done
2024-07-23 19:40:45.007197 INFO::Found NA in Reference column
2024-07-23 19:40:45.022794 INFO::Require at least two references per batch.
2024-07-23 19:40:45.04868 INFO::Formatting Data.
2024-07-23 19:40:45.04953 INFO::Recognized SummarizedExperiment
2024-07-23 19:40:45.050081 INFO::Typecasting input to dataframe.
2024-07-23 19:40:45.062412 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.06384 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.067872 INFO::Found 0 missing values.
2024-07-23 19:40:45.07799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.078915 INFO::Done
2024-07-23 19:40:45.099258 INFO::Formatting Data.
2024-07-23 19:40:45.100053 INFO::Recognized SummarizedExperiment
2024-07-23 19:40:45.100798 INFO::Typecasting input to dataframe.
2024-07-23 19:40:45.120143 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.121781 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.127122 INFO::Found 0 missing values.
2024-07-23 19:40:45.141655 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.142432 INFO::Done
2024-07-23 19:40:45.163919 INFO::Formatting Data.
2024-07-23 19:40:45.165066 INFO::Recognized SummarizedExperiment
2024-07-23 19:40:45.16578 INFO::Typecasting input to dataframe.
2024-07-23 19:40:45.190092 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.191666 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.193483 INFO::Found 0 missing values.
2024-07-23 19:40:45.194873 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-23 19:40:45.200335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.201182 INFO::Done
2024-07-23 19:40:45.217699 INFO::Formatting Data.
2024-07-23 19:40:45.218674 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.21971 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.220943 INFO::Found 0 missing values.
2024-07-23 19:40:45.22403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.224561 INFO::Done
2024-07-23 19:40:45.243261 INFO::Formatting Data.
2024-07-23 19:40:45.244531 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.24595 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.24751 INFO::Found 0 missing values.
2024-07-23 19:40:45.252056 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.252659 INFO::Done
2024-07-23 19:40:45.297246 INFO::Formatting Data.
2024-07-23 19:40:45.29808 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.299219 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.300929 INFO::Found 1 missing values.
2024-07-23 19:40:45.30516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.305891 INFO::Done
2024-07-23 19:40:45.335672 INFO::Formatting Data.
2024-07-23 19:40:45.336518 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.337542 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.33877 INFO::Found 2 missing values.
2024-07-23 19:40:45.340018 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2024-07-23 19:40:45.343272 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.343832 INFO::Done
2024-07-23 19:40:45.359055 INFO::Formatting Data.
2024-07-23 19:40:45.360189 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.361356 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.362287 INFO::Found 2 missing values.
2024-07-23 19:40:45.364431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.364933 INFO::Done
2024-07-23 19:40:45.382935 INFO::Formatting Data.
2024-07-23 19:40:45.384163 INFO::Typecasting input to dataframe.
2024-07-23 19:40:45.385514 INFO::Replacing NaNs with NAs.
2024-07-23 19:40:45.386901 INFO::Removing potential empty rows and columns
2024-07-23 19:40:45.388003 INFO::Found 0 missing values.
2024-07-23 19:40:45.392481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-23 19:40:45.393357 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
21.531 4.067 26.106
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 28.752 | 1.622 | 20.748 | |
| compute_asw | 0.028 | 0.003 | 0.031 | |
| count_existing | 0.015 | 0.001 | 0.018 | |
| generate_data_covariables | 0.017 | 0.001 | 0.019 | |
| generate_dataset | 0.015 | 0.001 | 0.017 | |